Mercurial > repos > recetox > rmassbank

annotate createSettingsFile.py @ 2:94d6243033ec draft default tip

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
author recetox
date Thu, 18 May 2023 13:00:47 +0000
parents ef3965a6b927
children
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ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
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1 import sys
ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
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2
ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
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3 # Script that creates a .ini settings file for RMassBank pipeline
ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
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4 # 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
ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
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5 # INPUT: mysettings.ini (default file downloaded via R package RMassBank, will be stored in the docker)
ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
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6 #
ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
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7 # 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
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8
ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
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9 fin = open(sys.argv[1], "r")
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10 fout = open("mysettings_galaxy.ini", "wt")
ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
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11 for line in fin:
ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
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12 if "rtMargin:" in line:
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13 fout.write("rtMargin: " + sys.argv[2] + "\n")
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14 elif "rtShift:" in line:
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15 fout.write("rtShift: " + sys.argv[3] + "\n")
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16 elif "babeldir:" in line and "#" not in line:
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17 fout.write("babeldir: '" + sys.argv[32] + "'\n")
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18 elif "use_version:" in line:
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19 fout.write("use_version: " + sys.argv[4] + "\n")
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20 elif "use_rean_peaks:" in line:
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21 fout.write("use_rean_peaks: " + sys.argv[5] + "\n")
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22 elif "add_annotation:" in line:
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23 fout.write("add_annotation: " + sys.argv[6] + "\n")
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24 elif "include_sp_tags:" in line:
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25 fout.write("include_sp_tags: " + sys.argv[33] + "\n")
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26 elif "pH:" in line:
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27 fout.write(" pH: " + sys.argv[7] + " # [M+H]+: Accession numbers 1-14\n")
ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
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28 elif "pM:" in line:
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29 fout.write(" pM: " + sys.argv[8] + " # [M]+: 17-30\n")
ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
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30 elif "pNa:" in line:
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31 fout.write(" pNa: " + sys.argv[9] + " # [M+Na]+: 33-46\n")
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32 elif "mH:" in line:
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33 fout.write(" mH: " + sys.argv[10] + " # [M-H]-: 51-64\n")
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34 elif "mFA:" in line:
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35 fout.write(" mFA: " + sys.argv[11] + " # [M+FA]-: 67-80\n")
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36 elif "electronicNoiseWidth:" in line:
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37 fout.write("electronicNoiseWidth: " + sys.argv[12] + "\n")
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38 elif "recalibrateBy:" in line:
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39 fout.write("recalibrateBy: " + sys.argv[13] + "\n")
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40 elif "recalibrateMS1:" in line:
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41 fout.write("recalibrateMS1: " + sys.argv[14] + "\n")
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42 elif "recalibrateMS1Window:" in line:
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43 fout.write("recalibrateMS1Window: " + sys.argv[15] + "\n")
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44 elif "multiplicityFilter:" in line:
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45 fout.write("multiplicityFilter: " + sys.argv[16] + "\n")
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46 elif "ppmHighMass:" in line:
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47 fout.write(" ppmHighMass: " + sys.argv[17] + "\n")
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48 elif "ppmLowMass:" in line:
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49 fout.write(" ppmLowMass: " + sys.argv[18] + "\n")
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50 elif "massRangeDivision:" in line:
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51 fout.write(" massRangeDivision: " + sys.argv[19] + "\n")
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52 elif "ppmFine:" in line:
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53 fout.write(" ppmFine: " + sys.argv[20] + "\n")
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54 elif "prelimCut:" in line:
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55 fout.write(" prelimCut: " + sys.argv[21] + "\n")
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56 elif "prelimCutRatio:" in line:
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57 fout.write(" prelimCutRatio: " + sys.argv[22] + "\n")
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58 elif "fineCut:" in line:
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59 fout.write(" fineCut: " + sys.argv[23] + "\n")
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60 elif "fineCutRatio:" in line:
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61 fout.write(" fineCutRatio: " + sys.argv[24] + "\n")
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62 elif "specOkLimit:" in line:
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63 fout.write(" specOkLimit: " + sys.argv[25] + "\n")
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64 elif "dbeMinLimit:" in line:
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65 fout.write(" dbeMinLimit: " + sys.argv[26] + "\n")
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66 elif "satelliteMzLimit:" in line:
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67 fout.write(" satelliteMzLimit: " + sys.argv[27] + "\n")
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68 elif "satelliteIntLimit:" in line:
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69 fout.write(" satelliteIntLimit: " + sys.argv[28] + "\n")
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70 elif "ppmFine:" in line:
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71 fout.write(" ppmFine: " + sys.argv[29] + "\n")
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72 elif "mzCoarse:" in line:
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73 fout.write(" mzCoarse: " + sys.argv[30] + "\n")
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74 elif "fillPrecursorScan:" in line:
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75 fout.write(" fillPrecursorScan: " + sys.argv[31] + "\n")
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76 elif "unknownMass:" in line:
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77 fout.write("unknownMass: " + sys.argv[34] + "\n")
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78 else:
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79 fout.write(line)
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80 fin.close()
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81 fout.close()