- <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
+ <runnerClassName>compbio.runner.msa.ClustalO</runnerClassName>\r
+\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
+\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
+\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
+\r
+ <prmSeparator>=</prmSeparator>\r
+\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
+\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
+\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