| Previous changeset 1:da4192d32e10 (2020-02-13) Next changeset 3:b959fd359a6b (2020-02-16) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4" |
|
modified:
hyphy_fade.xml macros.xml |
| b |
| diff -r da4192d32e10 -r f65e8fe7d5b8 hyphy_fade.xml --- a/hyphy_fade.xml Thu Feb 13 15:02:39 2020 -0500 +++ b/hyphy_fade.xml Fri Feb 14 16:46:01 2020 -0500 |
| [ |
| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy0"> +<tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy1"> <description>: FUBAR* Approach to Directional Evolution (*Fast Unconstrained Bayesian Approximation)</description> <macros> @@ -9,7 +9,7 @@ <command detect_errors="exit_code"><![CDATA[ ln -s '$input_file' fade_input.fa && ln -s '$input_nhx' fade_input.nhx && - @HYPHY_INVOCATION@ fade + hyphy fade --alignment ./fade_input.fa --tree ./fade_input.nhx --branches '$branches' @@ -23,6 +23,7 @@ --burn-in '$samples' --samples '$samples_per_chain' #end if + --output '$fade_output' > '$fade_log' ]]></command> <inputs> @@ -49,7 +50,7 @@ </inputs> <outputs> <data name="fade_log" format="txt"/> - <data name="fade_output" format="hyphy_results.json" from_work_dir="fade_input.fa.FADE.json"/> + <data name="fade_output" format="hyphy_results.json" /> </outputs> <tests> <test> |
| b |
| diff -r da4192d32e10 -r f65e8fe7d5b8 macros.xml --- a/macros.xml Thu Feb 13 15:02:39 2020 -0500 +++ b/macros.xml Fri Feb 14 16:46:01 2020 -0500 |
| [ |
| @@ -80,6 +80,7 @@ <yield/> </requirements> </xml> + <token name="@HYPHYMPI@">mpirun -np \${GALAXY_SLOTS:-1} HYPHYMPI</token> <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which hyphy` && export HYPHY_PATH=`dirname \$HYPHY` && export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]></token> |