Mercurial > repos > iuc > hyphy_relax
annotate hyphy_relax.xml @ 28:be29e2137d32 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 9fa2234b56facaf70fce12e5c60638d801997594"
author | iuc |
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date | Fri, 18 Jun 2021 15:33:17 +0000 |
parents | a4c5dc437558 |
children | 3415a580926d |
rev | line source |
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551616a65f8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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1 <?xml version="1.0"?> |
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a4c5dc437558
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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2 <tool id="hyphy_relax" name="HyPhy-RELAX" version="@VERSION@+galaxy1" profile="19.09"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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3 <description>Detect relaxed selection in a codon-based |
551616a65f8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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4 phylogenetic framework</description> |
551616a65f8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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5 <macros> |
551616a65f8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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6 <import>macros.xml</import> |
551616a65f8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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7 </macros> |
551616a65f8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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8 <expand macro="requirements"/> |
551616a65f8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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9 <command detect_errors="exit_code"><![CDATA[ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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10 @SYMLINK_FILES@ |
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b8bdfac5a326
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8f76cb8602f79412152a92b267ee016605ae6b8e"
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11 export OMP_NUM_THREADS="\${GALAXY_SLOTS:-1}" && |
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8e92afe83af9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
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12 hyphy relax |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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13 --alignment ./$input_file |
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a4c5dc437558
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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14 @INPUT_TREE@ |
a4c5dc437558
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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15 --models '$models' |
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b8bdfac5a326
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8f76cb8602f79412152a92b267ee016605ae6b8e"
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16 --code '$gencodeid' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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17 --test '$test' |
a4c5dc437558
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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18 #if $reference: |
a4c5dc437558
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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19 --reference '$reference' |
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551616a65f8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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20 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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21 @advanced_options@ |
a4c5dc437558
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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22 --output '$relax_output' |
a4c5dc437558
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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23 @ERRORS@ |
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551616a65f8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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24 ]]></command> |
551616a65f8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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25 <inputs> |
551616a65f8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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26 <expand macro="inputs"/> |
551616a65f8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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27 <expand macro="gencode"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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28 <param argument="--models" type="select" label="Analysis Type" > |
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551616a65f8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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29 <option value="All">All</option> |
551616a65f8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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30 <option value="Minimal">Minimal</option> |
551616a65f8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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31 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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32 <param argument="--test" type="text" value="Unlabeled branches" optional="false" label="Branches to use as the test set"> |
a4c5dc437558
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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33 <sanitizer invalid_char=""> |
a4c5dc437558
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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34 <valid initial="default" /> |
a4c5dc437558
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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35 </sanitizer> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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36 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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37 <param argument="--reference" type="text" optional="true" label="Branches to use as the reference set"> |
a4c5dc437558
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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38 <sanitizer invalid_char=""> |
a4c5dc437558
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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39 <valid initial="default" /> |
a4c5dc437558
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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40 </sanitizer> |
a4c5dc437558
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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41 </param> |
a4c5dc437558
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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42 <expand macro="srv" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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43 </inputs> |
551616a65f8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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44 <outputs> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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45 <data name="relax_output" format="hyphy_results.json"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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46 <expand macro="alternative_model_output" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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47 </outputs> |
551616a65f8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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48 <tests> |
551616a65f8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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49 <test> |
551616a65f8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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50 <param name="input_file" ftype="fasta" value="relax-in1.fa"/> |
551616a65f8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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51 <param name="input_nhx" ftype="nhx" value="relax-in1.nhx"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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52 <param name="test" value="TEST" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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53 <output name="relax_output" file="relax-out1.json" compare="sim_size"/> |
551616a65f8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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54 </test> |
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55 <test> |
a4c5dc437558
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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56 <param name="input_file" ftype="nex" value="relax-in2.nex"/> |
a4c5dc437558
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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57 <param name="srv_options" value="specify" /> |
a4c5dc437558
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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58 <param name="save_alternative_model" value="true" /> |
a4c5dc437558
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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59 <param name="test" value="PR" /> |
a4c5dc437558
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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60 <param name="srv" value="Yes" /> |
a4c5dc437558
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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61 <output name="relax_output" file="relax-out2-1.json" compare="sim_size"/> |
a4c5dc437558
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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62 <output name="alternative_model" file="relax-out2-2.json" compare="sim_size"/> |
a4c5dc437558
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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63 </test> |
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64 </tests> |
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65 <help><![CDATA[ |
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66 RELAX: a test for selection differences |
7827dfb71693
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67 ======================================= |
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68 |
7827dfb71693
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69 What question does this method answer? |
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70 -------------------------------------- |
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71 |
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72 Is there evidence the strength of selection has been relaxed (or conversely intensified) on a specified group of lineages (TEST) |
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73 relative to a set of reference lineages (RELAX)? Importantly, RELAX is not designed to detect diversifying selection specifically. |
7827dfb71693
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74 We note that the RELAX framework can perform both this specific hypothesis test as well as fit a suite of descriptive models which address, |
7827dfb71693
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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75 or example, overall rate differences between test and reference branches or lineage-specific inferences of selection relaxation. |
7827dfb71693
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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76 |
7827dfb71693
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77 Recommended Applications |
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78 ------------------------ |
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79 |
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80 1. Testing for a systematic shift (relaxation / intensification) in the distribution of selection pressure associated with major biological transitions such as hosting switching in viruses, lifestyle evolution in bacteria (i.e. transition from free-living to endosymbiotic lifestyle |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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81 2. Comparing selective regimes between two subsets of branches in the tree, e.g. to investigate selective differences due an environmental/phenotypic changes. |
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82 |
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83 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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84 Brief description |
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85 ----------------- |
7827dfb71693
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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86 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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87 RELAX (a random effects test of selection relaxation) uses a random |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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88 effects branch-site model framework to test whether a set of 'Test' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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89 branches evolves under relaxed selection relative to a set of |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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90 'Reference' branches (R), as measured by the relaxation parameter (K). |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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91 |
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92 Input |
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93 ----- |
1
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94 |
5
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95 1. A *FASTA* sequence alignment. |
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96 2. A phylogenetic tree in the *Newick* format that is further partitioned into one or two groups (_TEST_ or _TEST_ and _REFERENCE_). See http://hyphy.org/tutorials/phylotree/ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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97 |
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98 Note: the names of sequences in the alignment must match the names of the sequences in the tree. |
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99 |
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100 |
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101 Output |
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102 ------ |
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103 |
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104 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf). |
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105 |
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106 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/RELAX for an example) |
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107 |
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108 Further reading |
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109 --------------- |
1
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110 |
5
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111 http://hyphy.org/methods/selection-methods/#RELAX |
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112 |
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113 |
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114 Tool options |
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115 ------------ |
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116 :: |
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117 |
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118 |
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119 --code Which genetic code to use |
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120 |
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121 --model Which type of test to run |
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122 All : fit 4 different models [default] |
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123 Minimal: only perform a 2-model test of relaxation/intensification [faster] |
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124 |
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125 |
0
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126 ]]></help> |
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127 <expand macro="citations"> |
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128 <citation type="doi">10.1093/molbev/msu400</citation> |
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129 </expand> |
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130 </tool> |