Mercurial > repos > iuc > hyphy_absrel
diff macros.xml @ 24:9275e81b5590 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
| author | iuc |
|---|---|
| date | Tue, 20 Apr 2021 10:30:06 +0000 |
| parents | 5a7c56a5cc08 |
| children | 5f2ca10db92a |
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--- a/macros.xml Fri Apr 09 21:51:00 2021 +0000 +++ b/macros.xml Tue Apr 20 10:30:06 2021 +0000 @@ -1,8 +1,8 @@ <?xml version="1.0"?> <macros> <xml name="inputs"> - <param name="input_file" type="data" format="fasta" label="Input FASTA file"/> - <param name="input_nhx" type="data" format="nhx" label="Input newick file"/> + <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" help="If the input file type is NEXUS and it includes a valid newick tree, that tree will override an uploaded newick tree" /> + <param name="input_nhx" type="data" format="nhx,newick" optional="true" label="Input newick file"/> </xml> <xml name="substitution"> <param name="model" type="select" label="Substitution model"> @@ -107,7 +107,7 @@ <yield/> </citations> </xml> - <token name="@VERSION@">2.5.30</token> + <token name="@VERSION@">2.5.31</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">hyphy</requirement> @@ -115,10 +115,14 @@ </requirements> </xml> <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token> - <token name="@CATCH_MPIERR@"><![CDATA[ + <token name="@CATCH_ERROR@"><![CDATA[ EC=\$? ; if [ \$EC -ne 0 ] ; then - cat errors.log.mpinode0 >&2 ; + if [ -f errors.log.mpinode0 ] ; then + cat errors.log.mpinode0 >&2 ; + else + cat errors.log >&2 ; + fi ; fi ; exit \$EC ]]></token> @@ -129,4 +133,12 @@ <token name="@HYPHY_INVOCATION@"><![CDATA[ @HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB ]]></token> + <token name="@SYMLINK_FILES@"><![CDATA[ + ln -s '$input_file' input.$input_file.extension && + ln -s '$@operation@_output' input.${input_file.extension}.@OPERATION@.json && + #set $input_file = 'input.%s' % $input_file.extension + #if $input_nhx: + ln -s '$input_nhx' input.nhx && + #end if + ]]></token> </macros>