Re-design jpred.pl input options: no -seq for a file with 1 FASTA record only.

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

diff --git a/conf/settings/JpredParameters.xml b/conf/settings/JpredParameters.xml
index 3697e70..365ffcd 100644 (file)
--- a/conf/settings/JpredParameters.xml
+++ b/conf/settings/JpredParameters.xml
@@ -15,21 +15,12 @@
     <options>\r
         <name>JABAWS configuration</name>\r
         <description>\r
-            Configure Jpred to worik within JABAWS\r
+            Configure Jpred to work within JABAWS\r
         </description>\r
         <optionNames>-jabaws</optionNames>\r
         <furtherDetails>prog_docs/jpred.txt</furtherDetails>\r
     </options>\r
 \r
-    <options>\r
-        <name>Single sequence prediction</name>\r
-        <description>\r
-            Configure Jpred to worik within JABAWS\r
-        </description>\r
-        <optionNames>-seq</optionNames>\r
-        <furtherDetails>prog_docs/jpred.txt</furtherDetails>\r
-    </options>\r
-\r
     <prmSeparator> </prmSeparator>\r
 \r
     <parameters isRequired="false">\r
@@ -39,7 +30,7 @@
         </description>\r
         <optionNames>-dbpath</optionNames>\r
         <furtherDetails>prog_docs/jpred.txt</furtherDetails>\r
-        <defaultValue>.</defaultValue>\r
+        <defaultValue>/data/UNIREFdb</defaultValue>\r
      </parameters>\r
 \r
     <parameters isRequired="true">\r
@@ -53,19 +44,12 @@
         <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
+            Number of CPU used by Jpred. Maximum value is 8\r
         </description>\r
         <optionNames>-ncpu</optionNames>\r
         <furtherDetails>prog_docs/jpred.txt</furtherDetails>\r
@@ -77,13 +61,4 @@ experimental development databases:
         </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