Mercurial > repos > iuc > hyphy_fade
comparison hyphy_fade.xml @ 25:5e8d0e777033 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
author | iuc |
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date | Tue, 27 Apr 2021 18:06:34 +0000 |
parents | 17ac281a46d9 |
children | 96817f0fd28b |
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24:64380f4e296a | 25:5e8d0e777033 |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy0" profile="19.09"> | 2 <tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy1" profile="19.09"> |
3 <description>: FUBAR* Approach to Directional Evolution (*Fast | 3 <description>: FUBAR* Approach to Directional Evolution (*Fast |
4 Unconstrained Bayesian Approximation)</description> | 4 Unconstrained Bayesian Approximation)</description> |
5 <macros> | 5 <macros> |
6 <import>macros.xml</import> | 6 <import>macros.xml</import> |
7 <token name="@OPERATION@">FADE</token> | |
8 <token name="@operation@">fade</token> | |
9 </macros> | 7 </macros> |
10 <expand macro="requirements"/> | 8 <expand macro="requirements"/> |
11 <command detect_errors="exit_code"><![CDATA[ | 9 <command detect_errors="exit_code"><![CDATA[ |
12 @SYMLINK_FILES@ | 10 @SYMLINK_FILES@ |
13 hyphy fade | 11 hyphy fade |
14 --alignment ./$input_file | 12 --alignment $input_file |
15 #if $input_nhx: | 13 @INPUT_TREE@ |
16 --tree ./input.nhx | 14 @branch_options@ |
17 #end if | |
18 --branches '$branches' | |
19 --model '$model' | 15 --model '$model' |
20 --method '$posteriorEstimationMethod.method' | 16 --method '$posteriorEstimationMethod.method' |
21 --grid '$grid_points' | 17 --grid '$grid_points' |
22 --concentration_parameter '$concentration' | 18 --concentration_parameter '$concentration' |
23 @posteriorEstimationMethod_cmd@ | 19 @posteriorEstimationMethod_cmd@ |
24 --output '$fade_output' | 20 --output '$fade_output' |
25 > '$fade_log' ; | 21 @ERRORS@ |
26 @CATCH_ERROR@ | |
27 ]]></command> | 22 ]]></command> |
28 <inputs> | 23 <inputs> |
29 <expand macro="inputs"/> | 24 <expand macro="inputs"/> |
30 <expand macro="branches"/> | 25 <expand macro="branches"/> |
31 <expand macro="substitution"/> | 26 <expand macro="substitution"/> |
33 <expand macro="conditional_posteriorEstimationMethod" /> | 28 <expand macro="conditional_posteriorEstimationMethod" /> |
34 <param name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points"/> | 29 <param name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points"/> |
35 <param name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior"/> | 30 <param name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior"/> |
36 </inputs> | 31 </inputs> |
37 <outputs> | 32 <outputs> |
38 <data name="fade_log" format="txt"/> | |
39 <data name="fade_output" format="hyphy_results.json" /> | 33 <data name="fade_output" format="hyphy_results.json" /> |
40 </outputs> | 34 </outputs> |
41 <tests> | 35 <tests> |
42 <test> | 36 <test> |
43 <param name="input_file" ftype="fasta" value="fade-in1.fa"/> | 37 <param name="input_file" ftype="fasta" value="fade-in1.fa"/> |