Mercurial > repos > galaxyp > idpqonvert
changeset 2:e39c5664b04a draft
Uploaded
| author | galaxyp |
|---|---|
| date | Tue, 30 Sep 2014 15:31:54 -0400 |
| parents | 6cc571c2b3d1 |
| children | d1f7b2395bc2 |
| files | tools/idpqonvert.xml |
| diffstat | 1 files changed, 0 insertions(+), 21 deletions(-) [+] |
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--- 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 - --->