Mercurial > repos > iuc > hyphy_fel
annotate hyphy_fel.xml @ 33:8a6ef85b934d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
author | iuc |
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date | Wed, 30 Mar 2022 00:12:04 +0000 |
parents | fc50c4bac0a3 |
children | ec783806a5c3 |
rev | line source |
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24a2bf70dbdd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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1 <?xml version="1.0"?> |
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fc50c4bac0a3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
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2 <tool id="hyphy_fel" name="HyPhy-FEL" version="@TOOL_VERSION@+galaxy1" profile="19.09"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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3 <description>Fixed Effects Likelihood</description> |
24a2bf70dbdd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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4 <macros> |
24a2bf70dbdd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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5 <import>macros.xml</import> |
24a2bf70dbdd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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6 </macros> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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7 <expand macro="bio_tools"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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8 <expand macro="requirements"/> |
6c3ece5fb602
"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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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
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11 @HYPHYMPI@ fel |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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12 --alignment ./$input_file |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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13 @INPUT_TREE@ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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14 --code '$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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15 @branch_options@ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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16 --srv '$include_srv' |
6c3ece5fb602
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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17 --pvalue '$p_value' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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18 @resample@ |
8a6ef85b934d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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19 --precision $precision |
8a6ef85b934d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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20 $ci |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
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21 --output '$fel_output' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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22 @ERRORS@ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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23 ]]></command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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24 <inputs> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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25 <expand macro="inputs"/> |
6c3ece5fb602
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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26 <expand macro="gencode"/> |
6c3ece5fb602
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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27 <expand macro="branches"/> |
6c3ece5fb602
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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28 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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29 <param name="include_srv" type="select" label="Include synonymous rate variation" help = "Allow synonymous rates to vary from site to site"> |
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6c3ece5fb602
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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30 <option value="Yes">Yes (recommended)</option> |
6c3ece5fb602
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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31 <option value="No">No</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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32 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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33 <param argument="--ci" type="boolean" truevalue="--ci Yes" falsevalue="" label="Compute profile likelihood confidence intervals for each variable site" /> |
8a6ef85b934d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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34 <expand macro="resample"/> |
8a6ef85b934d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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35 <param argument="--precision" type="select" label="Optimization precision for preliminary fits"> |
8a6ef85b934d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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36 <option value="standard">Standard</option> |
8a6ef85b934d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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37 <option value="reduced">Reduced for faster fitting</option> |
8a6ef85b934d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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38 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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39 </inputs> |
24a2bf70dbdd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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40 <outputs> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
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41 <data name="fel_output" format="hyphy_results.json" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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42 </outputs> |
24a2bf70dbdd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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43 <tests> |
24a2bf70dbdd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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44 <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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45 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> |
6c3ece5fb602
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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46 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> |
6c3ece5fb602
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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47 <output name="fel_output" file="fel-out1.json" compare="sim_size"/> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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48 </test> |
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49 <test> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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50 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> |
8a6ef85b934d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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51 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> |
8a6ef85b934d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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52 <param name="ci" value="true" /> |
8a6ef85b934d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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53 <param name="precision" value="reduced" /> |
8a6ef85b934d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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54 <output name="fel_output" file="fel-out1.json" compare="sim_size"/> |
8a6ef85b934d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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55 </test> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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56 </tests> |
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57 <help><![CDATA[ |
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58 FEL : Fixed effects likelihood |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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59 ============================== |
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60 |
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61 What question does this method answer? |
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62 -------------------------------------- |
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63 |
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64 Which site(s) in a gene are subject to pervasive, i.e. consistently across the entire phylogeny, diversifying selection? |
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65 |
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66 Recommended Applications |
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67 ------------------------ |
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68 |
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69 The phenomenon of pervasive selection is generally most prevalent in pathogen evolution and any biological system influenced by evolutionary arms race dynamics |
8389039f7fbc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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70 (or balancing selection), including adaptive immune escape by viruses. As such, FEL is ideally suited to identify sites under positive selection which |
8389039f7fbc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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71 represent candidate sites subject to strong selective pressures across the entire phylogeny. |
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72 |
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73 FEL is our recommended method for analyzing small-to-medium size datasets when one wishes only to study pervasive selection at individual sites. |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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74 |
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75 Brief description |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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76 ----------------- |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
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77 |
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78 FEL (Fixed Effects Likelihood) estimates site-wise synonymous (alpha) |
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79 and non-synonymous rates (beta), and uses a likelihood ratio test to |
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80 determine if beta != alpha at a site. The estimates aggregate |
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81 information over all branches, so the signal is derived from pervasive |
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82 diversification or conservation. A subset of branches can be selected |
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83 for testing as well, in which case an additional (nuisance) parameter |
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84 will be inferred -- the non-synonymous rate on branches NOT selected for |
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85 testing. |
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86 |
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87 |
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88 Input |
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89 ----- |
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90 |
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91 1. A *FASTA* sequence alignment. |
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92 2. A phylogenetic tree in the *Newick* format |
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93 |
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94 Note: the names of sequences in the alignment must match the names of the sequences in the tree. |
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95 |
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96 |
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97 Output |
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98 ------ |
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99 |
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100 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf). |
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101 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/FEL for an example) |
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102 |
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103 Further reading |
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104 --------------- |
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105 |
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106 http://hyphy.org/methods/selection-methods/#FEL |
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107 |
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108 |
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109 Tool options |
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110 ------------ |
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111 |
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112 :: |
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113 |
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114 --code Which genetic code to use |
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115 |
6
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116 --branches Which branches should be tested for selection? |
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117 All [default] : test all branches |
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118 |
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119 Internal : test only internal branches (suitable for |
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120 intra-host pathogen evolution for example, where terminal branches |
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121 may contain polymorphism data) |
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122 |
6
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123 Leaves: test only terminal (leaf) branches |
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124 |
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125 Unlabeled: if the Newick string is labeled using the {} notation, |
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126 test only branches without explicit labels |
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127 (see http://hyphy.org/tutorials/phylotree/) |
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128 |
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129 --pvalue The significance level used to determine significance |
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130 |
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131 --srv Include site-to-site synonymous rate variation? |
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132 Yes [default] or No |
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133 |
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134 |
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135 |
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136 |
6
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137 ]]> |
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138 |
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139 </help> |
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140 |
0
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141 <expand macro="citations"> |
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142 <citation type="doi">10.1093/molbev/msi105</citation> |
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143 </expand> |
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144 </tool> |