Command line commands and parameters

Command line interface

qpMerge uses GNU style command line system. Use the "-h" option to get tool specific help.

All tools are called by the command

java -jar qpMerge.jar -p "tool" {other tool specific commands}

Currently the valid tool options for -p include

"RemoveIdenticalPeptides"
"ImportResourcesFromExperiment"
"MergeAlternativeModifications"
"MergeAlternativeTrypticDigests"
"MergeChargeStates"
"MergeIdenticalPeptides"
"RemoveUnmodifiedPeptides"
"MzQuantMLParser"
"CreateExperimentXML"
"TemplateMetaData"

An example workflow using command line only

Use the -h command to find out what each flag means.

Parse Arabidopsis metadata into an XML format qpMerge can understand

java -jar qpMerge.jar -p TemplateMetaData -t "METADATA.txt" -o "METADATA.xml"

Initial import of Arabidopsis data into qpMerge

java -jar qpMerge.jar -p ImportResourcesFromExperiment -i "METADATA.xml" -o "initialImport.xml" -t "xml" -pgi "Progenesis_Output_pr140404_at_ms131108_OGethyl-SDSethyl_all.csv" -fas "TAIR10_pep_20110103_representative_gene_model_updated.fasta"