Mercurial > repos > rdvelazquez > hyphy_busted

diff macros.xml @ 2:0d4341fca959 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
author rdvelazquez
date Mon, 11 Feb 2019 14:14:48 -0500
parents 8686dd081ecf
children d0a3511a8f33
line wrap: on
line diff
--- a/macros.xml	Tue Jan 08 10:56:06 2019 -0500
+++ b/macros.xml	Mon Feb 11 14:14:48 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>
@@ -13,9 +44,10 @@
             <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 ]]>
+export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]>
     </token>
-</macros>
\ No newline at end of file
+    <token name="@HYPHY_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ cat tool_params | HYPHYMP LIBPATH=\$HYPHY_LIB ]]></token>
+    <token name="@HYPHYMPI_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ cat tool_params | mpirun -np \${GALAXY_SLOTS:-1} HYPHYMPI LIBPATH=\$HYPHY_LIB ]]></token>
+</macros>