Repository revision
2:9ac2e8232c5c

Repository 'proteomiqon_psmstatistics'
hg clone https://toolshed.g2.bx.psu.edu/repos/galaxyp/proteomiqon_psmstatistics

ProteomIQon PSMStatistics tool metadata
Miscellaneous
utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.
proteomiqon_psmstatistics
toolshed.g2.bx.psu.edu/repos/galaxyp/proteomiqon_psmstatistics/proteomiqon_psmstatistics/0.0.8
0.0.8
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/galaxyp/proteomiqon_psmstatistics/proteomiqon_psmstatistics/0.0.8 (this tool)
toolshed.g2.bx.psu.edu/repos/galaxyp/proteomiqon_psmstatistics/proteomiqon_psmstatistics/0.0.7
toolshed.g2.bx.psu.edu/repos/galaxyp/proteomiqon_psmstatistics/proteomiqon_psmstatistics/0.0.6
proteomiqon_psmstatistics
Requirements (dependencies defined in the <requirements> tag set)
name version type
proteomiqon-psmstatistics 0.0.8 package
Additional information about this tool
#import re
        #set basename = $re.sub(r'[^\w ,.\-+]','_', $psm.element_identifier)
        #if $outputParamfile:
            cat '$paramfile' >> '$out_paramfile' &&
        #end if
        ln -s '$psm' '${basename}.psm' &&
        ln -s '$out_qpsm' '${basename}.qpsm' &&
        proteomiqon-psmstatistics -i './${basename}.psm' -d '$peptideDB' -p '$paramfile' -o ./
    
    
None
False
Functional tests
name inputs outputs required files
Test-1 psm: sample.psm
peptideDB: sample.db
ThresholdCond|QValueThreshold: 0.01
ThresholdCond|PepValueThreshold: 0.05
ThresholdCond|MaxIterations: 15
ThresholdCond|MinimumIncreaseBetweenIterations: 0.005
ThresholdCond|ProcessingType: Estimate
ParseProteinIDRegexPattern: id
outputParamfile: False
sample.psm
sample.db
Test-2 psm: sample.psm
peptideDB: sample.db
ThresholdCond|QValueThreshold: 0.01
ThresholdCond|PepValueThreshold: 0.05
ThresholdCond|MaxIterations: 15
ThresholdCond|MinimumIncreaseBetweenIterations: 0.005
ThresholdCond|ProcessingType: Estimate
ParseProteinIDRegexPattern: id
outputParamfile: True
name: value
sample.psm
sample.db
value
Test-3 psm: sample.psm
peptideDB: sample.db
ThresholdCond|QValueThreshold: 0.01
ThresholdCond|PepValueThreshold: 0.05
ThresholdCond|MaxIterations: 15
ThresholdCond|MinimumIncreaseBetweenIterations: 0.005
ThresholdCond|ProcessingType: Estimate
ParseProteinIDRegexPattern: id
outputParamfile: True
name: value
sample.psm
sample.db
value
Test-4 psm: sample.psm
peptideDB: sample.db
ThresholdCond|SequestLike: 5.0
ThresholdCond|Andromeda: 40.0
ThresholdCond|ProcessingType: Fixed
ParseProteinIDRegexPattern: id
outputParamfile: True
name: value
sample.psm
sample.db
value