diff macros.xml @ 1:0f108ee932ea draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"

--- a/macros.xml	Thu Jan 17 04:22:54 2019 -0500
+++ b/macros.xml	Wed Aug 21 12:24:34 2019 -0400
@@ -1,57 +1,87 @@
 <?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" label="Input FASTA file"/>
+        <param name="input_nhx" type="data" format="nhx" label="Input newick file"/>
+    </xml>
+    <xml name="substitution">
+        <param name="model" type="select" label="Substitution model">
+            <option value="LG">LG - Generalist empirical model from
+            Le and Gascuel (2008)</option>
+            <option value="HIVBm">HIVBm - Specialist empirical model
+            for between-host HIV sequences</option>
+            <option value="HIVWm">HIVWm - Specialist empirical model
+            for within-host HIV sequences</option>
+            <option value="WAG">WAG - Generalist empirical model from
+            Whelan and Goldman (2001)</option>
+            <option value="JTT">JTT - Generalist empirical model from
+            Jones, Taylor, and Thornton (1996)</option>
+            <option value="JC69">JC69 - Generalist empirical model
+            from with equal exchangeability rates</option>
+            <option value="mtMet">mtMet - Specialist empirical model
+            for metazoan mitochondrial genomes</option>
+            <option value="mtVer">mtVer - Specialist empirical model
+            for vertebrate mitochondrial genomes</option>
+            <option value="mtInv">mtInv - Specialist empirical model
+            for invertebrate mitochondrial genomes</option>
+            <option value="gcpREV">gcpREV - Specialist empirical
+            model for green plant chloroplast genomes</option>
+            <option value="GTR">GTR - General time reversible
+            model</option>
+        </param>
     </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>
+            <option value="Universal">Universal code</option>
+            <option value="Vertebrate-mtDNA">Vertebrate mitochondrial DNA
+            code</option>
+            <option value="Yeast-mtDNA">Yeast mitochondrial DNA
+            code</option>
+            <option value="Mold-Protozoan-mtDNA">Mold, Protozoan and
+            Coelenterate mt; Mycloplasma/Spiroplasma</option>
+            <option value="Invertebrate-mtDNA">Invertebrate mitochondrial
+            DNA code</option>
+            <option value="Ciliate-Nuclear">Ciliate, Dasycladacean and
+            Hexamita Nuclear code</option>
+            <option value="Echinoderm-mtDNA">Echinoderm mitochondrial DNA
+            code</option>
+            <option value="Euplotid-Nuclear">Euplotid Nuclear
+            code</option>
+            <option value="Alt-Yeast-Nuclear">Alternative Yeast Nuclear
+            code</option>
+            <option value="Ascidian-mtDNA">Ascidian mitochondrial DNA
+            code</option>
+            <option value="Flatworm-mtDNA">Flatworm mitochondrial DNA
+            code</option>
+            <option value="Blepharisma-Nuclear">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>
+            <option value="All">All branches</option>
+            <option value="Internal">Internal branches</option>
+            <option value="Leaves">Leaf branches</option>
+            <option value="'Unlabeled-branches'">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 />
+            <yield/>
         </citations>
     </xml>
-    <token name="@VERSION@">2.3.14</token>
+    <token name="@VERSION@">2.5.0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@VERSION@">hyphy</requirement>
-            <yield />
+            <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 hyphy` &&
 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@ hyphy LIBPATH=\$HYPHY_LIB ]]></token>
+</macros>