I would like to find features (small molecules) for my *.mzXML.inspect files by batch, yet I can't quite get the syntax of the for command right. Here's what I have typed:
for %%f in (C:\Users\bennetsa\Documents\Obesity-CKD_Project\Metabolite_Data_110810\*.mzXML.inspect) do java -Xmx2048m -jar C:\viewerApp_2010_11_10_1209.jar --findPeptides --out=C:\Users\bennetsa\Documents\Obesity-CKD_Project\Metabolite_Data_110810\%%f.peptides.tsv --strategy=FeatureStrategySmallMolecule --minMZ=99 --maxMz=2000 The error message (repeated for each file in the folder) is: Failure while parsing arguments: Missing Required unnamed series of parameters for command findpeptides findpeptides [--accuratemassscans=<integer>] [--count=<integer>] [--dumpwindow=< integer>] [--format=<msinspect | apml | hardklor>] [--maxkl=<decimal>] [--maxmz= <decimal>] [--minmz=<decimal>] [--minpeaks=<integer>] [--noaccuratemass=<true | false>] [--nofilter=<true | false>] [--out=<filepath>] [--outdir=<filepath>] [-- plotstats=<true | false>] [--start=<integer>] [--strategy=<value>] [--walksmooth ed=<true | false>] <filepath> <filepath> ... I thought these parameters were default and did not need to be enumerated. Assistance would be greatly appreciated! Sincerely, Sam Bennett -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
