annotate addBabelPath.py @ 1:c1a9c990d4b0 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
author recetox
date Thu, 12 Oct 2023 13:31:44 +0000
parents 0b28816c1c2c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
recetox
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1 import sys
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
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0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
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3 # Script that replaces OpenBabel path in settings file used within Galaxy (tools installed via conda)#
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
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4 # python script.py /path/settings_file /babeldir/path
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
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0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
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6 fin = open(sys.argv[1], "r")
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
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7 fout = open("mysettings_galaxy.ini", "wt")
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
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0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
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9 for line in fin:
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
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10 if "babeldir:" in line and "#" not in line:
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
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11 fout.write("babeldir: '" + sys.argv[2] + "'\n")
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
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12 else:
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
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13 fout.write(line)
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
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14 fin.close()
0b28816c1c2c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8
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15 fout.close()