Merge branch 'JABAWS_Release_2_5' into develop

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

diff --git a/conf/settings/ClustaloParameters.xml b/conf/settings/ClustaloParameters.xml
index 711011e..0a1be98 100644 (file)
--- a/conf/settings/ClustaloParameters.xml
+++ b/conf/settings/ClustaloParameters.xml
@@ -1,59 +1,66 @@
 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
 <runnerConfig>\r
-       <runnerClassName>compbio.runner.msa.ClustalO</runnerClassName>\r
-       <options>\r
-               <name>Dealign</name>\r
-               <description>Dealign input sequences</description>\r
-               <optionNames>--dealign</optionNames>\r
-               <furtherDetails>prog_docs/clustalo.txt</furtherDetails>\r
-       </options>\r
-       <options>\r
-               <name>Full distance matrix</name>\r
-               <description>Use full distance matrix for guide-tree calculation (slow; mBed is default)</description>\r
-               <optionNames>--full</optionNames>\r
-               <furtherDetails>prog_docs/clustalo.txt</furtherDetails>\r
-       </options>\r
-       <options>\r
-               <name>Full distance matrix for each iteration</name>\r
-               <description>Use full distance matrix for guide-tree calculation during iteration (mBed is default)</description>\r
-               <optionNames>--full-iter</optionNames>\r
-               <furtherDetails>prog_docs/clustalo.txt</furtherDetails>\r
-       </options>\r
-       <prmSeparator>=</prmSeparator>\r
-       <parameters>\r
-               <name>Max Guide tree iterations</name>\r
-               <description>Maximum number of HMM iterations</description>\r
-               <optionNames>--max-hmm-iterations</optionNames>\r
-               <furtherDetails>prog_docs/clustalo.txt</furtherDetails>\r
-               <defaultValue>1</defaultValue>\r
-               <validValue>\r
-                       <type>Integer</type>\r
-                       <min>1</min>\r
-                       <max>100</max>\r
-               </validValue>\r
-       </parameters>\r
-       <parameters>\r
-               <name>Number of iterations (combined)</name>\r
-               <description>Number of (combined guide tree/HMM) iterations</description>\r
-               <optionNames>--iter</optionNames>\r
-               <furtherDetails>prog_docs/clustalo.txt</furtherDetails>\r
-               <defaultValue>1</defaultValue>\r
-               <validValue>\r
-                       <type>Integer</type>\r
-                       <min>1</min>\r
-                       <max>100</max>\r
-               </validValue>\r
-       </parameters>\r
-       <parameters>\r
-               <name>Max Guide tree iterations</name>\r
-               <description>Maximum guide tree iterations</description>\r
-               <optionNames>--max-guidetree-iterations</optionNames>\r
-               <furtherDetails>prog_docs/clustalo.txt</furtherDetails>\r
-               <defaultValue>1</defaultValue>\r
-               <validValue>\r
-                       <type>Integer</type>\r
-                       <min>1</min>\r
-                       <max>100</max>\r
-               </validValue>\r
-       </parameters>\r
+    <runnerClassName>compbio.runner.msa.ClustalO</runnerClassName>\r
+\r
+    <options>\r
+        <name>Dealign</name>\r
+        <description>Dealign input sequences</description>\r
+        <optionNames>--dealign</optionNames>\r
+        <furtherDetails>prog_docs/clustalo.txt</furtherDetails>\r
+    </options>\r
+\r
+    <options>\r
+        <name>Full distance matrix</name>\r
+        <description>Use full distance matrix for guide-tree calculation (slow; mBed is default)</description>\r
+        <optionNames>--full</optionNames>\r
+        <furtherDetails>prog_docs/clustalo.txt</furtherDetails>\r
+    </options>\r
+\r
+    <options>\r
+        <name>Full distance matrix for each iteration</name>\r
+        <description>Use full distance matrix for guide-tree calculation during iteration (mBed is default)</description>\r
+        <optionNames>--full-iter</optionNames>\r
+        <furtherDetails>prog_docs/clustalo.txt</furtherDetails>\r
+    </options>\r
+\r
+    <prmSeparator>=</prmSeparator>\r
+\r
+    <parameters>\r
+        <name>Max Guide tree iterations</name>\r
+        <description>Maximum number of HMM iterations</description>\r
+        <optionNames>--max-hmm-iterations</optionNames>\r
+        <furtherDetails>prog_docs/clustalo.txt</furtherDetails>\r
+        <defaultValue>1</defaultValue>\r
+        <validValue>\r
+            <type>Integer</type>\r
+            <min>1</min>\r
+            <max>100</max>\r
+        </validValue>\r
+    </parameters>\r
+\r
+    <parameters>\r
+        <name>Number of iterations (combined)</name>\r
+        <description>Number of (combined guide tree/HMM) iterations</description>\r
+        <optionNames>--iter</optionNames>\r
+        <furtherDetails>prog_docs/clustalo.txt</furtherDetails>\r
+        <defaultValue>1</defaultValue>\r
+        <validValue>\r
+            <type>Integer</type>\r
+            <min>1</min>\r
+            <max>100</max>\r
+        </validValue>\r
+    </parameters>\r
+\r
+    <parameters>\r
+        <name>Max Guide tree iterations</name>\r
+        <description>Maximum guide tree iterations</description>\r
+        <optionNames>--max-guidetree-iterations</optionNames>\r
+        <furtherDetails>prog_docs/clustalo.txt</furtherDetails>\r
+        <defaultValue>1</defaultValue>\r
+        <validValue>\r
+            <type>Integer</type>\r
+            <min>1</min>\r
+            <max>100</max>\r
+        </validValue>\r
+    </parameters>\r
 </runnerConfig>\r