diff macros.xml @ 15:296f6bc03fa6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"

--- a/macros.xml	Fri Apr 09 21:51:27 2021 +0000
+++ b/macros.xml	Tue Apr 20 10:30:38 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>