diff macros.xml @ 0:fe399429a5d2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea

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+++ b/macros.xml	Thu Jan 17 04:22:54 2019 -0500
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+<?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>
+            <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` &&
+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>
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