Mercurial > repos > iuc > hyphy_busted
comparison hyphy_busted.xml @ 3:1d8b63d18f30 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
author | iuc |
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date | Fri, 14 Feb 2020 16:43:12 -0500 |
parents | f8d88dcef64e |
children | d6389faa75ff |
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2:f8d88dcef64e | 3:1d8b63d18f30 |
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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"> | 2 <tool id="hyphy_busted" name="HyPhy-BUSTED" version="@VERSION@+galaxy1"> |
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 </macros> | 6 </macros> |
7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
9 ln -s '$input_file' busted_input.fa && | 9 ln -s '$input_file' busted_input.fa && |
10 ln -s '$input_nhx' busted_input.nhx && | 10 ln -s '$input_nhx' busted_input.nhx && |
11 @HYPHY_INVOCATION@ busted | 11 hyphy busted |
12 --alignment ./busted_input.fa | 12 --alignment ./busted_input.fa |
13 --tree ./busted_input.nhx | 13 --tree ./busted_input.nhx |
14 --code $gencodeid | 14 --code $gencodeid |
15 --branches '$branches' | 15 --branches '$branches' |
16 --output '$busted_output' | |
16 > '$busted_log' | 17 > '$busted_log' |
17 ]]></command> | 18 ]]></command> |
18 <inputs> | 19 <inputs> |
19 <expand macro="inputs"/> | 20 <expand macro="inputs"/> |
20 <expand macro="gencode"/> | 21 <expand macro="gencode"/> |
21 <expand macro="branches"/> | 22 <expand macro="branches"/> |
22 </inputs> | 23 </inputs> |
23 <outputs> | 24 <outputs> |
24 <data name="busted_log" format="txt"/> | 25 <data name="busted_log" format="txt"/> |
25 <data name="busted_output" format="hyphy_results.json" from_work_dir="busted_input.fa.BUSTED.json"/> | 26 <data name="busted_output" format="hyphy_results.json" /> |
26 </outputs> | 27 </outputs> |
27 <tests> | 28 <tests> |
28 <test> | 29 <test> |
29 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> | 30 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> |
30 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> | 31 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> |