Mercurial > repos > recetox > rmassbank

annotate addBabelPath.py @ 1:6fa3c0ba2e66 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
author recetox
date Fri, 28 Jan 2022 16:31:11 +0000
parents ef3965a6b927
children
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
parents:
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
parents:
diff changeset
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
parents:
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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
parents:
diff changeset
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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diff changeset
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()