diff macros.xml @ 6:32b1229ad002 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f937b10585fe4b760772a6f1a7af20b428be9878-dirty

--- a/macros.xml	Thu Jan 17 14:07:01 2019 -0500
+++ b/macros.xml	Mon Feb 11 14:46:34 2019 -0500
@@ -1,5 +1,36 @@
 <?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"/>
+  </xml>
+  <xml name="gencode">
+    <param name="gencodeid" type="select" label="Genetic code">
+      <option value="1">Universal code</option>
+      <option value="2">Vertebrate mitochondrial DNA code</option>
+      <option value="3">Yeast mitochondrial DNA code</option>
+      <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option>
+      <option value="5">Invertebrate mitochondrial DNA code</option>
+      <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option>
+      <option value="7">Echinoderm mitochondrial DNA code</option>
+      <option value="8">Euplotid Nuclear code</option>
+      <option value="9">Alternative Yeast Nuclear code</option>
+      <option value="10">Ascidian mitochondrial DNA code</option>
+      <option value="11">Flatworm mitochondrial DNA code</option>
+      <option value="12">Blepharisma Nuclear code</option>
+    </param>
+  </xml>
+  <xml name="branches">
+    <param name="branches" type="select" label="Set of branches to test">
+      <option value="1">All branches</option>
+      <option value="2">Internal branches</option>
+      <option value="3">Leaf branches</option>
+      <option value="4">Unlabeled branches</option>
+    </param>
+  </xml>
+  <xml name="version_command">
+    <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command>
+  </xml>
   <xml name="citations">
     <citations>
       <citation type="doi">10.1093/bioinformatics/bti079</citation>
@@ -9,13 +40,16 @@
   <token name="@VERSION@">2.3.14</token>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="@VERSION@">
-      hyphy</requirement>
+      <requirement type="package" version="@VERSION@">hyphy</requirement>
       <yield/>
     </requirements>
   </xml>
-  <token name="@HYPHY_INVOCATION@"><![CDATA[export HYPHY=`which HYPHYMP` &&
+  <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which HYPHYMP` &&
 export HYPHY_PATH=`dirname \$HYPHY` &&
-export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&
-cat tool_params | HYPHYMP LIBPATH=\$HYPHY_LIB ]]></token>
+export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]></token>
+  <token name="@HYPHY_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ cat tool_params | HYPHYMP LIBPATH=\$HYPHY_LIB ]]></token>
+  <token name="@HYPHYMPI_INVOCATION@"><![CDATA[export HYPHYMPI=`which HYPHYMPI` &&
+export HYPHYMPI_PATH=`dirname \$HYPHYMPI` &&
+export HYPHYMPI_LIB=`readlink -f \$HYPHYMPI_PATH/../lib/hyphy` &&
+cat tool_params | mpirun -np \${GALAXY_SLOTS:-2} HYPHYMPI LIBPATH=\$HYPHYMPI_LIB ]]></token>
 </macros>