Mercurial > repos > iuc > hyphy_busted
comparison hyphy_busted.xml @ 26:70fab57f3c05 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 18:06:02 +0000 |
parents | e2f03a50aace |
children | d723b65a4291 |
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25:b6509de48a62 | 26:70fab57f3c05 |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <tool id="hyphy_busted" name="HyPhy-BUSTED" version="@VERSION@+galaxy0" profile="19.09"> | 2 <tool id="hyphy_busted" name="HyPhy-BUSTED" version="@VERSION@+galaxy1" profile="19.09"> |
3 <description>Branch-site Unrestricted Statistical Test for Episodic Diversification</description> | 3 <description>Branch-site Unrestricted Statistical Test for Episodic Diversification</description> |
4 <macros> | 4 <macros> |
5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
6 <token name="@OPERATION@">BUSTED</token> | |
7 <token name="@operation@">busted</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@ |
12 hyphy busted | 10 hyphy busted |
13 --alignment ./$input_file | 11 --alignment ./$input_file |
14 #if $input_nhx: | 12 @INPUT_TREE@ |
15 --tree ./input.nhx | |
16 #end if | |
17 --code $gencodeid | 13 --code $gencodeid |
18 --branches '$branches' | 14 @branch_options@ |
19 --output '$busted_output' | 15 --output '$busted_output' |
20 > '$busted_log' ; | 16 @advanced_options@ |
21 @CATCH_ERROR@ | 17 @ERRORS@ |
22 ]]></command> | 18 ]]></command> |
23 <inputs> | 19 <inputs> |
24 <expand macro="inputs"/> | 20 <expand macro="inputs"/> |
25 <expand macro="gencode"/> | 21 <expand macro="gencode"/> |
26 <expand macro="branches"/> | 22 <expand macro="branches"/> |
23 <expand macro="srv"/> | |
27 </inputs> | 24 </inputs> |
28 <outputs> | 25 <outputs> |
29 <data name="busted_log" format="txt"/> | |
30 <data name="busted_output" format="hyphy_results.json" /> | 26 <data name="busted_output" format="hyphy_results.json" /> |
27 <expand macro="alternative_model_output" /> | |
31 </outputs> | 28 </outputs> |
32 <tests> | 29 <tests> |
33 <test> | 30 <test> |
34 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> | 31 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> |
35 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> | 32 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> |
36 <output name="busted_output" file="busted-out1.json" compare="sim_size"/> | 33 <output name="busted_output" file="busted-out1.json" compare="sim_size"/> |
34 </test> | |
35 <test> | |
36 <param name="input_file" ftype="nex" value="busted-in2.nex"/> | |
37 <param name="branches" value="specify" /> | |
38 <param name="branch_label" value="B_US_90_WEAU160" /> | |
39 <param name="srv_options" value="specify" /> | |
40 <param name="save_alternative_model" value="true" /> | |
41 <output name="busted_output" file="busted-out2-1.json" compare="sim_size"/> | |
42 <output name="alternative_model" file="busted-out2-2.json" compare="sim_size"/> | |
37 </test> | 43 </test> |
38 </tests> | 44 </tests> |
39 <help><![CDATA[ | 45 <help><![CDATA[ |
40 | 46 |
41 BUSTED : Bayesian UnresTricted Test of Episodic Diversification | 47 BUSTED : Bayesian UnresTricted Test of Episodic Diversification |