Add testing dirs

[proteocache.git] / testsrc / testdata / TcoffeePresets.xml

diff --git a/testsrc/testdata/TcoffeePresets.xml b/testsrc/testdata/TcoffeePresets.xml
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+++ b/testsrc/testdata/TcoffeePresets.xml
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+<?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
+       <!-- These presets require BLAST and PDB database to be installed correctly neither of these works\r
+       at the moment\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
+        -->\r
+        <!-- \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
+       <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
+</presets>\r