Mercurial > repos > iuc > hyphy_fubar
comparison hyphy_fubar.xml @ 24:c5ef306c2041 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
| author | iuc |
|---|---|
| date | Tue, 20 Apr 2021 10:24:45 +0000 |
| parents | 3db56014322f |
| children | cd41e7a4d35f |
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| 23:f9f0518a0053 | 24:c5ef306c2041 |
|---|---|
| 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@+galaxy0" 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> | |
| 6 </macros> | 8 </macros> |
| 7 <expand macro="requirements"/> | 9 <expand macro="requirements"/> |
| 8 <command detect_errors="exit_code"><![CDATA[ | 10 <command detect_errors="exit_code"><![CDATA[ |
| 9 ln -s '$input_file' fubar_input.fa && | 11 @SYMLINK_FILES@ |
| 10 ln -s '$input_nhx' fubar_input.nhx && | |
| 11 hyphy fubar | 12 hyphy fubar |
| 12 --alignment ./fubar_input.fa | 13 --alignment ./$input_file |
| 13 --tree ./fubar_input.nhx | 14 #if $input_nhx: |
| 15 --tree ./input.nhx | |
| 16 #end if | |
| 14 --code '$gencodeid' | 17 --code '$gencodeid' |
| 15 --method '$posteriorEstimationMethod.method' | 18 --method '$posteriorEstimationMethod.method' |
| 16 --grid '$grid_points' | 19 --grid '$grid_points' |
| 17 @posteriorEstimationMethod_cmd@ | 20 @posteriorEstimationMethod_cmd@ |
| 18 --concentration_parameter '$concentration' | 21 --concentration_parameter '$concentration' |
| 19 > '$fubar_log' | 22 > '$fubar_log' ; |
| 23 @CATCH_ERROR@ | |
| 20 ]]></command> | 24 ]]></command> |
| 21 <inputs> | 25 <inputs> |
| 22 <expand macro="inputs"/> | 26 <expand macro="inputs"/> |
| 23 <expand macro="gencode"/> | 27 <expand macro="gencode"/> |
| 24 <param argument="--grid" name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points" /> | 28 <param argument="--grid" name="grid_points" type="integer" value="20" min="5" max="50" label="Grid points" /> |
| 26 <param argument="--concentration_parameter" name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior" /> | 30 <param argument="--concentration_parameter" name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior" /> |
| 27 | 31 |
| 28 </inputs> | 32 </inputs> |
| 29 <outputs> | 33 <outputs> |
| 30 <data name="fubar_log" format="txt"/> | 34 <data name="fubar_log" format="txt"/> |
| 31 <data name="fubar_output" format="hyphy_results.json" from_work_dir="fubar_input.fa.FUBAR.json" /> | 35 <data name="fubar_output" format="hyphy_results.json" /> |
| 32 </outputs> | 36 </outputs> |
| 33 <tests> | 37 <tests> |
| 34 <test> | 38 <test> |
| 35 <param name="input_file" ftype="fasta" value="fubar-in1.fa"/> | 39 <param name="input_file" ftype="fasta.gz" value="fubar-in1.fa.gz"/> |
| 36 <param name="input_nhx" ftype="nhx" value="fubar-in1.nhx"/> | 40 <param name="input_nhx" ftype="nhx" value="fubar-in1.nhx"/> |
| 37 <param name="posterior" value="Variational-Bayes"/> | 41 <param name="posterior" value="Variational-Bayes"/> |
| 38 <output name="fubar_output" file="fubar-out1.json" compare="sim_size"/> | 42 <output name="fubar_output" file="fubar-out1.json" compare="sim_size"/> |
| 39 </test> | 43 </test> |
| 40 </tests> | 44 </tests> |