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 |
|---|---|
| date | Tue, 27 Apr 2021 18:06:02 +0000 |
| parents | e2f03a50aace |
| children | d723b65a4291 |
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| 25:b6509de48a62 | 26:70fab57f3c05 |
|---|---|
| 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 |