Mercurial > repos > iuc > hyphy_fubar
comparison hyphy_fubar.xml @ 26:cd41e7a4d35f 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 18:04:56 +0000 |
parents | c5ef306c2041 |
children | 099fc3ec12d2 |
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25:296409764676 | 26:cd41e7a4d35f |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <tool id="hyphy_fubar" name="HyPhy-FUBAR" version="@VERSION@+galaxy0" profile="19.09"> | 2 <tool id="hyphy_fubar" name="HyPhy-FUBAR" version="@VERSION@+galaxy1" profile="19.09"> |
3 <description>Fast Unconstrained Bayesian AppRoximation</description> | 3 <description>Fast Unconstrained Bayesian AppRoximation</description> |
4 <macros> | 4 <macros> |
5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
6 <token name="@OPERATION@">FUBAR</token> | |
7 <token name="@operation@">fubar</token> | |
8 </macros> | 6 </macros> |
9 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
10 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
11 @SYMLINK_FILES@ | 9 @SYMLINK_FILES@ |
10 ln -s '$fubar_output' ${input_file}.FUBAR.json && | |
12 hyphy fubar | 11 hyphy fubar |
13 --alignment ./$input_file | 12 --alignment ./$input_file |
14 #if $input_nhx: | 13 @INPUT_TREE@ |
15 --tree ./input.nhx | |
16 #end if | |
17 --code '$gencodeid' | 14 --code '$gencodeid' |
18 --method '$posteriorEstimationMethod.method' | 15 --method '$posteriorEstimationMethod.method' |
19 --grid '$grid_points' | 16 --grid '$grid_points' |
20 @posteriorEstimationMethod_cmd@ | 17 @posteriorEstimationMethod_cmd@ |
21 --concentration_parameter '$concentration' | 18 --concentration_parameter '$concentration' |
22 > '$fubar_log' ; | 19 @ERRORS@ |
23 @CATCH_ERROR@ | |
24 ]]></command> | 20 ]]></command> |
25 <inputs> | 21 <inputs> |
26 <expand macro="inputs"/> | 22 <expand macro="inputs"/> |
27 <expand macro="gencode"/> | 23 <expand macro="gencode"/> |
28 <param argument="--grid" name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points" /> | 24 <param argument="--grid" name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points" /> |
29 <expand macro="conditional_posteriorEstimationMethod" /> | 25 <expand macro="conditional_posteriorEstimationMethod" /> |
30 <param argument="--concentration_parameter" name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior" /> | 26 <param argument="--concentration_parameter" name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior" /> |
31 | 27 |
32 </inputs> | 28 </inputs> |
33 <outputs> | 29 <outputs> |
34 <data name="fubar_log" format="txt"/> | |
35 <data name="fubar_output" format="hyphy_results.json" /> | 30 <data name="fubar_output" format="hyphy_results.json" /> |
36 </outputs> | 31 </outputs> |
37 <tests> | 32 <tests> |
38 <test> | 33 <test> |
39 <param name="input_file" ftype="fasta.gz" value="fubar-in1.fa.gz"/> | 34 <param name="input_file" ftype="fasta.gz" value="fubar-in1.fa.gz"/> |