<runnerClassName>compbio.runner.disorder.Disembl</runnerClassName>\r
<prmSeparator>=</prmSeparator>\r
<parameters>\r
- <name>Default parameters should not be changed!</name>\r
- <description>Normally the default parameters should not be changed. \r
- If the query protein sequence is very long, >1000 residues, you can download the predictions and \r
- use a local graph/plotting tool such as Grace or OpenOffice.org to plot and zoom the data. \r
- Having identified the potential disordered regions, you should now have a good basis for setting \r
- up expression vectors and/or comparing the data with obtained structural data. \r
- </description>\r
- <optionNames>-sg</optionNames>\r
+ <name>Savitzky-Golay smoothing frame</name>\r
+ <description>Algorithm Parameter: Savitzky-Golay smoothing frame</description>\r
+ <optionNames>sg</optionNames>\r
<furtherDetails>prog_docs/disembl.html</furtherDetails>\r
- <defaultValue>1</defaultValue>\r
+ <defaultValue>8</defaultValue>\r
+ <validValue>\r
+ <type>Integer</type>\r
+ <min>1</min>\r
+ <max>30</max>\r
+ </validValue>\r
</parameters>\r
-</runnerConfig>\r
+<!-- \r
+ These can be supported but not recommended to change so what's the point?\r
\r
-
\ No newline at end of file
+ Manual: Normally the default parameters should not be changed.\r
+\r
+ <parameters>\r
+ <name>Minimum peak width</name>\r
+ <description>Algorithm Parameter: Minimum peak width.</description>\r
+ <optionNames>pw</optionNames>\r
+ <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
+ <defaultValue>8</defaultValue>\r
+ <validValue>\r
+ <type>Integer</type>\r
+ <min>1</min>\r
+ <max>30</max>\r
+ </validValue>\r
+ </parameters>\r
+ <parameters>\r
+ <name>Maximum join distance</name>\r
+ <description>Algorithm Parameter: Maximum join distance</description>\r
+ <optionNames>jd</optionNames>\r
+ <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
+ <defaultValue>4</defaultValue>\r
+ <validValue>\r
+ <type>Integer</type>\r
+ <min>1</min>\r
+ <max>30</max>\r
+ </validValue>\r
+ </parameters>\r
+ <parameters>\r
+ <name>Coils threshold</name>\r
+ <description>Stringency values for different predictor: Coils threshold</description>\r
+ <optionNames>ct</optionNames>\r
+ <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
+ <defaultValue>1.2</defaultValue>\r
+ <validValue>\r
+ <type>Float</type>\r
+ <min>0.1</min>\r
+ <max>10</max>\r
+ </validValue>\r
+ </parameters>\r
+ <parameters>\r
+ <name>Remark465 threshold</name>\r
+ <description>Stringency values for different predictor: Remark465 threshold</description>\r
+ <optionNames>rt</optionNames>\r
+ <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
+ <defaultValue>1.4</defaultValue>\r
+ <validValue>\r
+ <type>Float</type>\r
+ <min>0.1</min>\r
+ <max>10</max>\r
+ </validValue>\r
+ </parameters>\r
+ <parameters>\r
+ <name>Hot loops threshold</name>\r
+ <description>Stringency values for different predictor: Hot loops threshold.</description>\r
+ <optionNames>lt</optionNames>\r
+ <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
+ <defaultValue>1.2</defaultValue>\r
+ <validValue>\r
+ <type>Float</type>\r
+ <min>0.1</min>\r
+ <max>10</max>\r
+ </validValue>\r
+ </parameters>\r
+ -->\r
+\r
+</runnerConfig>\r