Mercurial > repos > recetox > rmassbank

annotate addBabelPath.py @ 0:ef3965a6b927 draft

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"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
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
recetox
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diff changeset
1 import sys
ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
recetox
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ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
recetox
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3 # Script that replaces OpenBabel path in settings file used within Galaxy (tools installed via conda)#
ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
recetox
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4 # python script.py /path/settings_file /babeldir/path
ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
recetox
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ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
recetox
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6 fin = open(sys.argv[1], "r")
ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
recetox
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7 fout = open("mysettings_galaxy.ini", "wt")
ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
recetox
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8
ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
recetox
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9 for line in fin:
ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
recetox
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10 if "babeldir:" in line and "#" not in line:
ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
recetox
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11 fout.write("babeldir: '" + sys.argv[2] + "'\n")
ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
recetox
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12 else:
ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
recetox
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13 fout.write(line)
ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
recetox
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14 fin.close()
ef3965a6b927 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 683f472a44f296d65cf572a5e720839fc4c0141e"
recetox
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15 fout.close()