| Previous changeset 2:de93e1fbdc31 (2020-02-13) Next changeset 4:181f5b9f139f (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_absrel.xml macros.xml |
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| diff -r de93e1fbdc31 -r fb40b0928cad hyphy_absrel.xml --- a/hyphy_absrel.xml Thu Feb 13 15:01:22 2020 -0500 +++ b/hyphy_absrel.xml Fri Feb 14 16:44:41 2020 -0500 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy0"> +<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy1"> <description>adaptive Branch Site Random Effects Likelihood</description> <macros> <import>macros.xml</import> @@ -8,12 +8,15 @@ <command detect_errors="exit_code"><![CDATA[ ln -s '$input_file' absrel_input.fa && ln -s '$input_nhx' absrel_input.nhx && - @HYPHY_INVOCATION@ absrel + @HYPHYMPI@ absrel --alignment ./absrel_input.fa --tree ./absrel_input.nhx --code '$gencodeid' --branches '$branches' - > '$absrel_log' + --output '$absrel_output' + #if $log: + > '$absrel_log' + #end if ]]></command> <inputs> <expand macro="inputs"/> @@ -25,7 +28,7 @@ <data name="absrel_log" format="txt"> <filter>log</filter> </data> - <data name="absrel_output" format="hyphy_results.json" from_work_dir="absrel_input.fa.ABSREL.json"/> + <data name="absrel_output" format="hyphy_results.json" /> </outputs> <tests> <test> |
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| diff -r de93e1fbdc31 -r fb40b0928cad macros.xml --- a/macros.xml Thu Feb 13 15:01:22 2020 -0500 +++ b/macros.xml Fri Feb 14 16:44:41 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> |