Clustal Omega web service wrapper and tester

[jabaws.git] / testsrc / testdata / ClustaloParameters.xml

diff --git a/testsrc/testdata/ClustaloParameters.xml b/testsrc/testdata/ClustaloParameters.xml
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+<?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
+</runnerConfig>\r