| Previous changeset 2:a603e2f909e5 (2020-02-13) Next changeset 4:8522e7cc4fb4 (2020-02-16) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4" |
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modified:
hyphy_slac.xml macros.xml |
| b |
| diff -r a603e2f909e5 -r 242ed2357a01 hyphy_slac.xml --- a/hyphy_slac.xml Thu Feb 13 15:03:50 2020 -0500 +++ b/hyphy_slac.xml Fri Feb 14 16:47:07 2020 -0500 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="hyphy_slac" name="HyPhy-SLAC" version="@VERSION@+galaxy0"> +<tool id="hyphy_slac" name="HyPhy-SLAC" version="@VERSION@+galaxy1"> <description>Single Likelihood Ancestor Counting</description> <macros> <import>macros.xml</import> @@ -8,13 +8,14 @@ <command detect_errors="exit_code"><![CDATA[ ln -s '$input_file' slac_input.fa && ln -s '$input_nhx' slac_input.nhx && - @HYPHY_INVOCATION@ slac + hyphy slac --alignment ./slac_input.fa --tree ./slac_input.nhx --code '$gencodeid' --branches '$branches' --samples '$number_of_samples' --pvalue '$p_value' + --output '$slac_output' > '$slac_log' ]]></command> <inputs> @@ -26,7 +27,7 @@ </inputs> <outputs> <data name="slac_log" format="txt"/> - <data name="slac_output" format="hyphy_results.json" from_work_dir="slac_input.fa.SLAC.json"/> + <data name="slac_output" format="hyphy_results.json" /> </outputs> <tests> <test> |
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| diff -r a603e2f909e5 -r 242ed2357a01 macros.xml --- a/macros.xml Thu Feb 13 15:03:50 2020 -0500 +++ b/macros.xml Fri Feb 14 16:47:07 2020 -0500 |
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| @@ -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> |