Mercurial > repos > iuc > hyphy_relax
diff hyphy_relax.xml @ 23:18c32f4d11e0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
| author | iuc |
|---|---|
| date | Tue, 20 Apr 2021 10:21:12 +0000 |
| parents | 9d255b14885e |
| children | 69ba121e201c |
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--- a/hyphy_relax.xml Fri Apr 09 21:44:49 2021 +0000 +++ b/hyphy_relax.xml Tue Apr 20 10:21:12 2021 +0000 @@ -4,16 +4,18 @@ phylogenetic framework</description> <macros> <import>macros.xml</import> + <token name="@OPERATION@">RELAX</token> + <token name="@operation@">relax</token> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ - ln -s '$input_file' relax_input.fa && - ln -s '$input_nhx' relax_input.nhx && - + @SYMLINK_FILES@ export OMP_NUM_THREADS="\${GALAXY_SLOTS:-1}" && hyphy relax - --alignment ./relax_input.fa - --tree ./relax_input.nhx + --alignment ./$input_file + #if $input_nhx: + --tree ./input.nhx + #end if --models '$analysisType' --code '$gencodeid' #if $treeAnnotations == "2": @@ -22,7 +24,8 @@ #else: --test TEST #end if - > '$relax_log' + > '$relax_log' ; + @CATCH_ERROR@ ]]></command> <inputs> <expand macro="inputs"/> @@ -38,7 +41,7 @@ </inputs> <outputs> <data name="relax_log" format="txt"/> - <data name="relax_output" format="hyphy_results.json" from_work_dir="relax_input.fa.RELAX.json"/> + <data name="relax_output" format="hyphy_results.json"/> </outputs> <tests> <test>