diff macros.xml @ 3:3b7f2dbb5c44 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6e7f074d80e0f35516e223b76e73f019ad45dd74-dirty

--- a/macros.xml	Tue Oct 30 10:57:16 2018 -0400
+++ b/macros.xml	Wed Mar 06 14:31:33 2019 -0500
@@ -1,26 +1,55 @@
 <?xml version="1.0"?>
 <macros>
-    <xml name="citations">
-        <citations>
-            <citation type="doi">10.1093/bioinformatics/bti079</citation>
-            <yield />
-        </citations>
-    </xml>
-    <token name="@VERSION@">2.3.14</token>
-    <xml name="requirements">
-        <requirements>
-            <requirement type="package" version="@VERSION@">hyphy</requirement>
-            <yield />
-        </requirements>
-    </xml>
-    <token name="@HYPHY_INVOCATION@"><![CDATA[export HYPHY=`which HYPHYMP` &&
+  <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>
+      <yield/>
+    </citations>
+  </xml>
+  <token name="@VERSION@">2.3.14</token>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="@VERSION@">hyphy</requirement>
+      <yield/>
+    </requirements>
+  </xml>
+  <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>
-    <token name="@HYPHYMPI_INVOCATION@"><![CDATA[export HYPHY=`which HYPHYMP` &&
-export HYPHY_PATH=`dirname \$HYPHY` &&
-export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&
-cat tool_params | mpirun -np \${GALAXY_SLOTS:-1} HYPHYMPI LIBPATH=\$HYPHY_LIB ]]>
-    </token>
-</macros>
\ No newline at end of file
+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>