Merge branch 'JABAWS_Release_2_5' into develop

[jabaws.git] / conf / settings / TcoffeePresets.xml

diff --git a/conf/settings/TcoffeePresets.xml b/conf/settings/TcoffeePresets.xml
index 585bb21..646db9c 100644 (file)
--- a/conf/settings/TcoffeePresets.xml
+++ b/conf/settings/TcoffeePresets.xml
@@ -1,54 +1,61 @@
 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
 <presets>\r
-       <runnerClassName>compbio.runner.tcoffee.Tcoffee</runnerClassName>\r
-       <preset>\r
-               <name>Quick align. Very fast approximate (Speed-oriented)</name>\r
-               <description>quickaln: Very fast, sequence type - all, accuracy - medium low</description>\r
-               <optlist>\r
-                       <option>-mode quickaln</option>\r
-               </optlist>\r
-       </preset>\r
-       <!-- does not work\r
-       <preset>\r
-               <name>Dali (Speed-oriented)</name>\r
-               <description>dali: a mode used to combine dali pairwise alignments</description>\r
-               <optlist>\r
-                       <option>-mode dali</option>\r
-               </optlist>\r
-       </preset>\r
-       -->\r
-       <!-- This requires Blast to operate, however i do not know how to plug it to t-coffee. \r
-       The build in one does not work.  \r
-       <preset>\r
-               <name>3dcoffee (Accuracy-oriented)</name>\r
-               <description>3dcoffee: runs t_coffee with the 3dcoffee  parameterization</description>\r
-               <optlist>\r
-                       <option>-mode 3dcoffee</option>\r
-               </optlist>\r
-       </preset>\r
-       <preset>\r
-               <name>Accurate (Accuracy-oriented)</name>\r
-               <description>accurate: slow, sequence type - protein, accuracy - high</description>\r
-               <optlist>\r
-                       <option>-mode accurate</option>\r
-               </optlist>\r
-       </preset>\r
-       could not find templates(?)\r
-       <preset>\r
-               <name>Rcoffee for RNA only (accuracy-oriented)</name>\r
-               <description> rcoffee: slow, sequence type - RNA, accuracy - high</description>\r
-               <optlist>\r
-                       <option>-mode rcoffee</option>\r
-               </optlist>\r
-       </preset>\r
-        -->\r
-        <!-- This needs blast\r
-       <preset>\r
-               <name>Expresso (accuracy-oriented)</name>\r
-               <description> expresso: slow, sequence type - all, accuracy - high</description>\r
-               <optlist>\r
-                       <option>-mode expresso</option>\r
-               </optlist>\r
-       </preset>\r
-        --> \r
+    <runnerClassName>compbio.runner.msa.Tcoffee</runnerClassName>\r
+\r
+    <preset>\r
+        <name>Quick align. Very fast approximate (Speed-oriented)</name>\r
+        <description>quickaln: Very fast, sequence type - all, accuracy - medium low</description>\r
+        <optlist>\r
+            <option>-mode quickaln</option>\r
+        </optlist>\r
+    </preset>\r
+\r
+    <!-- does not work\r
+    <preset>\r
+        <name>Dali (Speed-oriented)</name>\r
+        <description>dali: a mode used to combine dali pairwise alignments</description>\r
+        <optlist>\r
+            <option>-mode dali</option>\r
+        </optlist>\r
+    </preset>\r
+    -->\r
+\r
+    <!-- This requires Blast to operate, however i do not know how to plug it to t-coffee. \r
+    The build in one does not work.  \r
+    <preset>\r
+        <name>3dcoffee (Accuracy-oriented)</name>\r
+        <description>3dcoffee: runs t_coffee with the 3dcoffee    parameterization</description>\r
+        <optlist>\r
+            <option>-mode 3dcoffee</option>\r
+        </optlist>\r
+    </preset>\r
+\r
+    <preset>\r
+        <name>Accurate (Accuracy-oriented)</name>\r
+        <description>accurate: slow, sequence type - protein, accuracy - high</description>\r
+        <optlist>\r
+            <option>-mode accurate</option>\r
+        </optlist>\r
+    </preset>\r
+\r
+    could not find templates(?)\r
+    <preset>\r
+        <name>Rcoffee for RNA only (accuracy-oriented)</name>\r
+        <description> rcoffee: slow, sequence type - RNA, accuracy - high</description>\r
+        <optlist>\r
+            <option>-mode rcoffee</option>\r
+        </optlist>\r
+    </preset>\r
+     -->\r
+\r
+    <!-- This needs blast\r
+    <preset>\r
+        <name>Expresso (accuracy-oriented)</name>\r
+        <description> expresso: slow, sequence type - all, accuracy - high</description>\r
+        <optlist>\r
+            <option>-mode expresso</option>\r
+        </optlist>\r
+    </preset>\r
+     -->\r
+\r
 </presets>\r