From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Tue, 14 Jun 2011 17:26:54 +0000 (+0000)
Subject: Adding XML executable description for IUPred
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4e6b482a5d99c5741394778d787986a4a67da403;p=jabaws.git

Adding XML executable description for IUPred

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4266 e3abac25-378b-4346-85de-24260fe3988d
---

diff --git a/conf/settings/IUPredLimits.xml b/conf/settings/IUPredLimits.xml
new file mode 100644
index 0000000..8d3a09f
--- /dev/null
+++ b/conf/settings/IUPredLimits.xml
@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
+<limits>
+ <runnerClassName>compbio.runner.disorder.IUPred</runnerClassName>
+	<limit isDefault="true">
+		<seqNumber>5000</seqNumber>
+		<seqLength>1000</seqLength>
+	</limit>
+	<limit isDefault="false">
+		<preset># LocalEngineExecutionLimit #</preset>
+		<seqNumber>200</seqNumber>
+		<seqLength>400</seqLength>
+	</limit>
+	<limit isDefault="false">
+		<preset>Quick conservation</preset>
+		<seqNumber>10000</seqNumber>
+		<seqLength>10000</seqLength>
+	</limit>
+	<limit isDefault="false">
+		<preset>Slow conservation</preset>
+		<seqNumber>2000</seqNumber>
+		<seqLength>1000</seqLength>
+	</limit>
+	<limit isDefault="false">
+		<preset>Complete conservation</preset>
+		<seqNumber>2000</seqNumber>
+		<seqLength>1000</seqLength>
+	</limit>
+</limits>
diff --git a/conf/settings/IUPredParameters.xml b/conf/settings/IUPredParameters.xml
new file mode 100644
index 0000000..1846cad
--- /dev/null
+++ b/conf/settings/IUPredParameters.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
+<runnerConfig>
+	<runnerClassName>compbio.runner.disorder.Disembl</runnerClassName>
+	<options isRequired="true">
+        <name>Disorder type</name>
+        <description></description>
+        <optionNames>short</optionNames>
+        <optionNames>long</optionNames>
+        <optionNames>glob</optionNames>
+        <furtherDetails>prog_docs/iupred.txt</furtherDetails>
+        <defaultValue>long</defaultValue>
+    </options>
+</runnerConfig>
diff --git a/conf/settings/IUPredPresets.xml b/conf/settings/IUPredPresets.xml
new file mode 100644
index 0000000..8cf8f44
--- /dev/null
+++ b/conf/settings/IUPredPresets.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
+<presets>
+ <runnerClassName>compbio.runner.disorder.IUPred</runnerClassName>
+	<preset>
+		<name>Complete Disorder</name>
+		<description>Short, Long disorder and globular domains</description>
+		<optlist>
+			<option>all</option>
+		</optlist>
+	</preset>
+</presets>
+
+
+
+ 
+