Merge branch 'JABAWS_Release_2_5' into develop

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

diff --git a/conf/settings/JpredParameters.xml b/conf/settings/JpredParameters.xml
new file mode 100644 (file)
index 0000000..ec4f167
--- /dev/null
+++ b/conf/settings/JpredParameters.xml
@@ -0,0 +1,80 @@
+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
+<runnerConfig>\r
+    <runnerClassName>compbio.runner.predictors.Jpred</runnerClassName>\r
+\r
+    <options>\r
+        <name>Prediction without PSI-BLAST hits</name>\r
+        <description>\r
+            Toggle allowing Jpred to make predictions even when there are no\r
+            PSI-BLAST hits.\r
+        </description>\r
+        <optionNames>-pred-nohits</optionNames>\r
+        <furtherDetails>prog_docs/jpred.txt</furtherDetails>\r
+    </options>\r
+\r
+    <options>\r
+        <name>JABAWS configuration</name>\r
+        <description>\r
+            Configure Jpred to worik within JABAWS\r
+        </description>\r
+        <optionNames>-jabaws</optionNames>\r
+        <furtherDetails>prog_docs/jpred.txt</furtherDetails>\r
+    </options>\r
+\r
+    <prmSeparator> </prmSeparator>\r
+\r
+    <parameters isRequired="false">\r
+        <name>UNIREF database</name>\r
+        <description>\r
+            Path to UNIREF database for PSI-BLAST querying\r
+        </description>\r
+        <optionNames>-dbpath</optionNames>\r
+        <furtherDetails>prog_docs/jpred.txt</furtherDetails>\r
+        <defaultValue>.</defaultValue>\r
+     </parameters>\r
+\r
+    <parameters isRequired="true">\r
+        <name>UNIREF database name</name>\r
+        <description>\r
+            Number of (combined guide tree/HMM) iterations\r
+        </description>\r
+        <optionNames>-dbname</optionNames>\r
+        <furtherDetails>prog_docs/jpred.txt</furtherDetails>\r
+        <defaultValue>ported_db</defaultValue>\r
+        <possibleValues>uniref90</possibleValues>\r
+        <possibleValues>ported_db</possibleValues>\r
+        <possibleValues>cluster</possibleValues>\r
+<!--\r
+experimental development databases:\r
+        <possibleValues>training</possibleValues>\r
+        <possibleValues>swall</possibleValues>\r
+        <possibleValues>uniprot</possibleValues>\r
+        <possibleValues>uniref50</possibleValues>\r
+-->\r
+    </parameters>\r
+\r
+     <parameters isRequired="false">\r
+        <name>Number of CPUs</name>\r
+        <description>\r
+            Number of CPU used by jpred.pl. Maximum value is 8\r
+        </description>\r
+        <optionNames>-ncpu</optionNames>\r
+        <furtherDetails>prog_docs/jpred.txt</furtherDetails>\r
+        <defaultValue>1</defaultValue>\r
+        <validValue>\r
+            <type>Integer</type>\r
+            <min>1</min>\r
+            <max>8</max>\r
+        </validValue>\r
+    </parameters>\r
+\r
+    <parameters isRequired="false">\r
+        <name>PSI-BLAST output file</name>\r
+        <description>\r
+            Path to a PSI-BLAST output file\r
+        </description>\r
+        <optionNames>-psi</optionNames>\r
+        <furtherDetails>prog_docs/jpred.txt</furtherDetails>\r
+        <defaultValue></defaultValue>\r
+    </parameters>\r
+</runnerConfig>\r