Mercurial > repos > recetox > rmassbank
diff createSettingsFile.py @ 0:ef3965a6b927 draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
| author | recetox |
|---|---|
| date | Thu, 04 Mar 2021 18:50:15 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/createSettingsFile.py Thu Mar 04 18:50:15 2021 +0000 @@ -0,0 +1,81 @@ +import sys + +# Script that creates a .ini settings file for RMassBank pipeline +# Intended to be wrapped as a tool to Galaxy (in docker) to create users of RMassBank the mysettings.ini file -> very "stupid" script, does not check correctness of user's input, that will do Galaxy XML wrapper +# INPUT: mysettings.ini (default file downloaded via R package RMassBank, will be stored in the docker) +# +# python script.py mysettings.ini 0.34 0.34 34 FALSE FALSE 34 34 34 34 34 0.34 dmz none 34 34 34 34 34 34 34 34 34 34 34 0.34 0.34 0.34 34 0.34 TRUE /babeldir/path FALSE charged + +fin = open(sys.argv[1], "r") +fout = open("mysettings_galaxy.ini", "wt") +for line in fin: + if "rtMargin:" in line: + fout.write("rtMargin: " + sys.argv[2] + "\n") + elif "rtShift:" in line: + fout.write("rtShift: " + sys.argv[3] + "\n") + elif "babeldir:" in line and "#" not in line: + fout.write("babeldir: '" + sys.argv[32] + "'\n") + elif "use_version:" in line: + fout.write("use_version: " + sys.argv[4] + "\n") + elif "use_rean_peaks:" in line: + fout.write("use_rean_peaks: " + sys.argv[5] + "\n") + elif "add_annotation:" in line: + fout.write("add_annotation: " + sys.argv[6] + "\n") + elif "include_sp_tags:" in line: + fout.write("include_sp_tags: " + sys.argv[33] + "\n") + elif "pH:" in line: + fout.write(" pH: " + sys.argv[7] + " # [M+H]+: Accession numbers 1-14\n") + elif "pM:" in line: + fout.write(" pM: " + sys.argv[8] + " # [M]+: 17-30\n") + elif "pNa:" in line: + fout.write(" pNa: " + sys.argv[9] + " # [M+Na]+: 33-46\n") + elif "mH:" in line: + fout.write(" mH: " + sys.argv[10] + " # [M-H]-: 51-64\n") + elif "mFA:" in line: + fout.write(" mFA: " + sys.argv[11] + " # [M+FA]-: 67-80\n") + elif "electronicNoiseWidth:" in line: + fout.write("electronicNoiseWidth: " + sys.argv[12] + "\n") + elif "recalibrateBy:" in line: + fout.write("recalibrateBy: " + sys.argv[13] + "\n") + elif "recalibrateMS1:" in line: + fout.write("recalibrateMS1: " + sys.argv[14] + "\n") + elif "recalibrateMS1Window:" in line: + fout.write("recalibrateMS1Window: " + sys.argv[15] + "\n") + elif "multiplicityFilter:" in line: + fout.write("multiplicityFilter: " + sys.argv[16] + "\n") + elif "ppmHighMass:" in line: + fout.write(" ppmHighMass: " + sys.argv[17] + "\n") + elif "ppmLowMass:" in line: + fout.write(" ppmLowMass: " + sys.argv[18] + "\n") + elif "massRangeDivision:" in line: + fout.write(" massRangeDivision: " + sys.argv[19] + "\n") + elif "ppmFine:" in line: + fout.write(" ppmFine: " + sys.argv[20] + "\n") + elif "prelimCut:" in line: + fout.write(" prelimCut: " + sys.argv[21] + "\n") + elif "prelimCutRatio:" in line: + fout.write(" prelimCutRatio: " + sys.argv[22] + "\n") + elif "fineCut:" in line: + fout.write(" fineCut: " + sys.argv[23] + "\n") + elif "fineCutRatio:" in line: + fout.write(" fineCutRatio: " + sys.argv[24] + "\n") + elif "specOkLimit:" in line: + fout.write(" specOkLimit: " + sys.argv[25] + "\n") + elif "dbeMinLimit:" in line: + fout.write(" dbeMinLimit: " + sys.argv[26] + "\n") + elif "satelliteMzLimit:" in line: + fout.write(" satelliteMzLimit: " + sys.argv[27] + "\n") + elif "satelliteIntLimit:" in line: + fout.write(" satelliteIntLimit: " + sys.argv[28] + "\n") + elif "ppmFine:" in line: + fout.write(" ppmFine: " + sys.argv[29] + "\n") + elif "mzCoarse:" in line: + fout.write(" mzCoarse: " + sys.argv[30] + "\n") + elif "fillPrecursorScan:" in line: + fout.write(" fillPrecursorScan: " + sys.argv[31] + "\n") + elif "unknownMass:" in line: + fout.write("unknownMass: " + sys.argv[34] + "\n") + else: + fout.write(line) +fin.close() +fout.close()