X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=conf%2Fsettings%2FClustaloParameters.xml;h=0a1be987bc6e15045c7ded7f66355dc0bab0b24b;hb=8907c35efd10d5968c0a64dba6a9524a2545df28;hp=711011e10c2550aed3b8e9f0a52e08a77cc894d9;hpb=35947b9e0b6ae1be74f17d15cd6a65ceadc6d310;p=jabaws.git

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