--- a/tools/idpqonvert.xml	Tue Sep 30 15:24:42 2014 -0400
+++ b/tools/idpqonvert.xml	Tue Sep 30 15:31:54 2014 -0400
@@ -4,7 +4,6 @@
     <requirement type="package" version="333">binaries_for_package_idpqonvert</requirement>
   </requirements>
 
-  <!-- TODO: Set defaults for weights correctly -->
   <description>
     Prepare identification results for IDPicker.
   </description>
@@ -49,8 +48,6 @@
     '${input_name}';
     mv '$output_name' output
   </command>
-<!-- idpQonvert needs spectrum available EmbedSpectrumScanTimes or EmbedSpectrumSources is set.
--->
   <stdio>
     <exit_code range="1:" level="fatal" description="Job Failed" />
     <regex match="^Could not find the default configuration file.*$"
@@ -190,21 +187,3 @@
   <help>
   </help>
 </tool>
-<!-- idpQonvert needs spectrum available EmbedSpectrumScanTimes or EmbedSpectrumSources is set.
-
-idpQonvert -OverwriteExistingFiles true -MaxFDR 0.05 -MaxImportFDR 0.25  -MaxResultRank 3 -RerankMatches false -TruePositiveThreshold 0.01 -MaxTrainingRank 1 -Gamma 5 -Nu -0.5 -PolynomialDegree 3 -ScoreInfo "1 off myrimatch:mvh; 1 off xcorr; 1 off sequest:xcorr; 1 off sequest:deltacn; 1 off mascot:score; -1 off xexpect; 1 off x\!tandem:hyperscore; -1 off ms-gf:specevalue" -SVMType CSVC -Kernel Linear -ChargeStateHandling Partition -QonverterMethod MonteCarlo -MinPartitionSize 10 -DecoyPrefix RRRRRR -ProteinDatabase test2.fasta input.pepXML
-
-
-ScoreInfo: 1 off myrimatch:mvh; 1 off xcorr; 1 off sequest:xcorr; 1 off sequest:deltacn; 1 off mascot:score; -1 off x!tandem:expect; 1 off x!tandem:hyperscore; -1 off ms-gf:specevalue
-
-off is normalization: quantile, linear, or off
-
-SVMType: CSVC, NuSVC, OneClass, EpsilonSVR, NuSVR
-Kernel: Linear, Polynomial, RBF (radial basis function), Sigmoid
-ChargeStateHandling: Parition, Ignore, Feature
-TerminalSpecificityHandling: Partition, Ignore, Feature
-MissedCleavagesHandling: Ignore, Feature
-MassErrorHandling: Ignore, Feature
-QonverterMethod: MonteCarlo, SingleSVM, PartitionedSVM, StaticWeighted
-
--->