<runnerClassName>compbio.runner.conservation.AACon</runnerClassName>\r
<options>\r
<name>Normalize</name>\r
- <description>Normalize the results. The results of the calculation by different methods will all be scaled to the range between 0 and 1, so that they are comparable</description>\r
+ <description>Normalize the results. \r
+ Normalized results have values between 0 and 1. Please note however, that \r
+ some results cannot be normalized. In such a case, the system returns not \r
+ normalized value. The following formula is used for normalization \r
+ n = (d - dmin)/(dmax - dmin)\r
+ Negative results first converted to positive by adding a greatest absolute \r
+ result value.</description>\r
<optionNames>-n</optionNames>\r
<furtherDetails>http://www.compbio.dundee.ac.uk/jabaws/prog_docs/aacon.txt</furtherDetails>\r
</options>\r
<possibleValues>VALDAR</possibleValues>\r
<possibleValues>SMERFS</possibleValues>\r
</parameters>\r
+ <parameters>\r
+ <name>SMERFS Window Width</name>\r
+ <description>The width of the window for SMERFS. Optional, defaults to 7</description>\r
+ <optionNames>-smerfsWW</optionNames>\r
+ <furtherDetails>http://www.compbio.dundee.ac.uk/jabaws/prog_docs/aacon.txt</furtherDetails>\r
+ <defaultValue>7</defaultValue>\r
+ <validValue>\r
+ <type>Integer</type>\r
+ <min>3</min>\r
+ <max>100</max>\r
+ </validValue>\r
+ </parameters>\r
+ <parameters>\r
+ <name>SMERFS Column Scoring Method</name>\r
+ <description>SMERFS Column Score algorithm defines the window scores to \r
+ columns allocation, two methods are possible:\r
+ MID_SCORE - gives the window score to the middle column\r
+ MAX_SCORE - gives the column the highest score of all the windows it \r
+ belongs to. Optional defaults to MID_SCORE. </description>\r
+ <optionNames>-smerfsCS</optionNames>\r
+ <furtherDetails>http://www.compbio.dundee.ac.uk/jabaws/prog_docs/aacon.txt</furtherDetails>\r
+ <defaultValue>MID_SCORE</defaultValue>\r
+ <possibleValues>MAX_SCORE</possibleValues>\r
+ <possibleValues>MID_SCORE</possibleValues>\r
+ </parameters>\r
+ <parameters>\r
+ <name>SMERFS Gap Threshhold</name>\r
+ <description>a gap percentage cutoff - a float greater than 0 and smaller or equal 1. Optional defaults to 0.1</description>\r
+ <optionNames>-smerfsGT</optionNames>\r
+ <furtherDetails>http://www.compbio.dundee.ac.uk/jabaws/prog_docs/aacon.txt</furtherDetails>\r
+ <defaultValue>0.1</defaultValue>\r
+ <validValue>\r
+ <type>Float</type>\r
+ <min>0.001</min>\r
+ <max>1</max>\r
+ </validValue>\r
+ </parameters>\r
</runnerConfig>\r