Mercurial > repos > iuc > hyphy_fubar
diff 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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--- a/hyphy_fubar.xml Fri Apr 09 21:48:06 2021 +0000 +++ b/hyphy_fubar.xml Tue Apr 20 10:24:45 2021 +0000 @@ -3,20 +3,24 @@ <description>Fast Unconstrained Bayesian AppRoximation</description> <macros> <import>macros.xml</import> + <token name="@OPERATION@">FUBAR</token> + <token name="@operation@">fubar</token> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ - ln -s '$input_file' fubar_input.fa && - ln -s '$input_nhx' fubar_input.nhx && + @SYMLINK_FILES@ hyphy fubar - --alignment ./fubar_input.fa - --tree ./fubar_input.nhx + --alignment ./$input_file + #if $input_nhx: + --tree ./input.nhx + #end if --code '$gencodeid' --method '$posteriorEstimationMethod.method' --grid '$grid_points' @posteriorEstimationMethod_cmd@ --concentration_parameter '$concentration' - > '$fubar_log' + > '$fubar_log' ; + @CATCH_ERROR@ ]]></command> <inputs> <expand macro="inputs"/> @@ -28,11 +32,11 @@ </inputs> <outputs> <data name="fubar_log" format="txt"/> - <data name="fubar_output" format="hyphy_results.json" from_work_dir="fubar_input.fa.FUBAR.json" /> + <data name="fubar_output" format="hyphy_results.json" /> </outputs> <tests> <test> - <param name="input_file" ftype="fasta" value="fubar-in1.fa"/> + <param name="input_file" ftype="fasta.gz" value="fubar-in1.fa.gz"/> <param name="input_nhx" ftype="nhx" value="fubar-in1.nhx"/> <param name="posterior" value="Variational-Bayes"/> <output name="fubar_output" file="fubar-out1.json" compare="sim_size"/>