Re-format configuration files

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

diff --git a/conf/settings/ClustalParameters.xml b/conf/settings/ClustalParameters.xml
index dde49d0..47b1d3f 100644 (file)
--- a/conf/settings/ClustalParameters.xml
+++ b/conf/settings/ClustalParameters.xml
@@ -1,25 +1,30 @@
 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
 <runnerConfig>\r
-    <runnerClassName>compbio.runner.clustal.ClustalW</runnerClassName>\r
+    <runnerClassName>compbio.runner.msa.ClustalW</runnerClassName>\r
+\r
     <options>\r
         <name>NOPGAP</name>\r
         <description>Residue-specific gaps off</description>\r
         <optionNames>-NOPGAP</optionNames>\r
         <furtherDetails>prog_docs/clustalw.txt</furtherDetails>\r
     </options>\r
+\r
     <options>\r
         <name>No transition weighting</name>\r
         <description>Disable sequence weighting</description>\r
         <optionNames>-NOWEIGHTS</optionNames>\r
         <furtherDetails>prog_docs/clustalw.txt</furtherDetails>\r
     </options>\r
+\r
     <options>\r
         <name>NOHGAP</name>\r
         <description>Hydrophilic gaps off</description>\r
         <optionNames>-NOHGAP</optionNames>\r
         <furtherDetails>prog_docs/clustalw.txt</furtherDetails>\r
     </options>\r
+\r
     <prmSeparator>=</prmSeparator>\r
+\r
     <parameters>\r
         <name>Transition weighting</name>\r
         <description>Type of the sequence (PROTEIN or DNA)</description>\r
@@ -32,6 +37,7 @@
             <max>10</max>\r
         </validValue>\r
     </parameters>\r
+\r
     <parameters>\r
         <name>Type</name>\r
         <description>Type of the sequence (PROTEIN or DNA)</description>\r
@@ -41,6 +47,7 @@
         <possibleValues>PROTEIN</possibleValues>\r
         <possibleValues>DNA</possibleValues>\r
     </parameters>\r
+\r
     <parameters>\r
         <name>OUTORDER</name>\r
         <description>As per INPUT or ALIGNED</description>\r
@@ -49,6 +56,7 @@
         <possibleValues>INPUT</possibleValues>\r
         <possibleValues>ALIGNED</possibleValues>\r
     </parameters>\r
+\r
     <parameters>\r
         <name>MATRIX</name>\r
         <description>Protein weight matrix</description>\r
@@ -134,6 +142,7 @@
         <possibleValues>PAM80</possibleValues>\r
         <possibleValues>PAM90</possibleValues>\r
     </parameters>\r
+\r
     <parameters>\r
         <name>GAPOPEN</name>\r
         <description>Gap opening penalty</description>\r
@@ -146,6 +155,7 @@
             <max>1000</max>\r
         </validValue>\r
     </parameters>\r
+\r
     <parameters>\r
         <name>-GAPEXT</name>\r
         <description>Gap extension penalty</description>\r
@@ -158,6 +168,7 @@
             <max>10</max>\r
         </validValue>\r
     </parameters>\r
+\r
     <parameters>\r
         <name>ENDGAPS</name>\r
         <description>End gap separation pen</description>\r
@@ -170,6 +181,7 @@
             <max>10</max>\r
         </validValue>\r
     </parameters>\r
+\r
     <parameters>\r
         <name>GAPDIST</name>\r
         <description>Gap separation pen. range</description>\r