Re-format configuration files

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

diff --git a/conf/settings/DisemblParameters.xml b/conf/settings/DisemblParameters.xml
index 676395e..c8b7c79 100644 (file)
--- a/conf/settings/DisemblParameters.xml
+++ b/conf/settings/DisemblParameters.xml
@@ -1,88 +1,89 @@
 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
 <runnerConfig>\r
-<!-- \r
-    Extreme variation of this parameter does not have any impact on the output\r
-    so irrelevant. \r
+<!--  Extreme variation of this parameter does not have any impact on the output so irrelevant.\r
+    <runnerClassName>compbio.runner.disorder.Disembl</runnerClassName>\r
+\r
+    <prmSeparator>=</prmSeparator>\r
+\r
+    <parameters>\r
+        <name>Savitzky-Golay smoothing frame</name>\r
+        <description>Algorithm Parameter: Savitzky-Golay smoothing frame</description>\r
+        <optionNames>sg</optionNames>\r
+        <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
+        <defaultValue>8</defaultValue>\r
+        <validValue>\r
+            <type>Integer</type>\r
+            <min>1</min>\r
+            <max>30</max>\r
+        </validValue>\r
+    </parameters>\r
 \r
-       <runnerClassName>compbio.runner.disorder.Disembl</runnerClassName>\r
-       <prmSeparator>=</prmSeparator>\r
-       <parameters>\r
-               <name>Savitzky-Golay smoothing frame</name>\r
-               <description>Algorithm Parameter: Savitzky-Golay smoothing frame</description>\r
-               <optionNames>sg</optionNames>\r
-               <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
-               <defaultValue>8</defaultValue>\r
-               <validValue>\r
-                       <type>Integer</type>\r
-                       <min>1</min>\r
-                       <max>30</max>\r
-               </validValue>\r
-       </parameters>\r
- \r
  These can be supported but not recommended to change so what's the point?\r
- \r
  Manual: Normally the default parameters should not be changed.\r
 \r
-       <parameters>\r
-               <name>Minimum peak width</name>\r
-               <description>Algorithm Parameter: Minimum peak width.</description>\r
-               <optionNames>pw</optionNames>\r
-               <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
-               <defaultValue>8</defaultValue>\r
-               <validValue>\r
-                       <type>Integer</type>\r
-                       <min>1</min>\r
-                       <max>30</max>\r
-               </validValue>\r
-       </parameters>\r
-       <parameters>\r
-               <name>Maximum join distance</name>\r
-               <description>Algorithm Parameter: Maximum join distance</description>\r
-               <optionNames>jd</optionNames>\r
-               <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
-               <defaultValue>4</defaultValue>\r
-               <validValue>\r
-                       <type>Integer</type>\r
-                       <min>1</min>\r
-                       <max>30</max>\r
-               </validValue>\r
-       </parameters>\r
-       <parameters>\r
-               <name>Coils threshold</name>\r
-               <description>Stringency values for different predictor: Coils threshold</description>\r
-               <optionNames>ct</optionNames>\r
-               <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
-               <defaultValue>1.2</defaultValue>\r
-               <validValue>\r
-                       <type>Float</type>\r
-                       <min>0.1</min>\r
-                       <max>10</max>\r
-               </validValue>\r
-       </parameters>\r
-       <parameters>\r
-               <name>Remark465 threshold</name>\r
-               <description>Stringency values for different predictor: Remark465 threshold</description>\r
-               <optionNames>rt</optionNames>\r
-               <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
-               <defaultValue>1.4</defaultValue>\r
-               <validValue>\r
-                       <type>Float</type>\r
-                       <min>0.1</min>\r
-                       <max>10</max>\r
-               </validValue>\r
-       </parameters>\r
-       <parameters>\r
-               <name>Hot loops threshold</name>\r
-               <description>Stringency values for different predictor: Hot loops threshold.</description>\r
-               <optionNames>lt</optionNames>\r
-               <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
-               <defaultValue>1.2</defaultValue>\r
-               <validValue>\r
-                       <type>Float</type>\r
-                       <min>0.1</min>\r
-                       <max>10</max>\r
-               </validValue>\r
-       </parameters>\r
-       -->\r
+    <parameters>\r
+        <name>Minimum peak width</name>\r
+        <description>Algorithm Parameter: Minimum peak width.</description>\r
+        <optionNames>pw</optionNames>\r
+        <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
+        <defaultValue>8</defaultValue>\r
+        <validValue>\r
+            <type>Integer</type>\r
+            <min>1</min>\r
+            <max>30</max>\r
+        </validValue>\r
+    </parameters>\r
+\r
+    <parameters>\r
+        <name>Maximum join distance</name>\r
+        <description>Algorithm Parameter: Maximum join distance</description>\r
+        <optionNames>jd</optionNames>\r
+        <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
+        <defaultValue>4</defaultValue>\r
+        <validValue>\r
+            <type>Integer</type>\r
+            <min>1</min>\r
+            <max>30</max>\r
+        </validValue>\r
+    </parameters>\r
+\r
+    <parameters>\r
+        <name>Coils threshold</name>\r
+        <description>Stringency values for different predictor: Coils threshold</description>\r
+        <optionNames>ct</optionNames>\r
+        <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
+        <defaultValue>1.2</defaultValue>\r
+        <validValue>\r
+            <type>Float</type>\r
+            <min>0.1</min>\r
+            <max>10</max>\r
+        </validValue>\r
+    </parameters>\r
+\r
+    <parameters>\r
+        <name>Remark465 threshold</name>\r
+        <description>Stringency values for different predictor: Remark465 threshold</description>\r
+        <optionNames>rt</optionNames>\r
+        <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
+        <defaultValue>1.4</defaultValue>\r
+        <validValue>\r
+            <type>Float</type>\r
+            <min>0.1</min>\r
+            <max>10</max>\r
+        </validValue>\r
+    </parameters>\r
 \r
+    <parameters>\r
+        <name>Hot loops threshold</name>\r
+        <description>Stringency values for different predictor: Hot loops threshold.</description>\r
+        <optionNames>lt</optionNames>\r
+        <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
+        <defaultValue>1.2</defaultValue>\r
+        <validValue>\r
+            <type>Float</type>\r
+            <min>0.1</min>\r
+            <max>10</max>\r
+        </validValue>\r
+    </parameters>\r
+-->\r
 </runnerConfig>\r