| Previous changeset 14:985ab0acd514 (2024-08-15) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1a24b53139f4c8370cf7ecc2bf8cce71cfe2663f |
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modified:
distance_finder.py ob_grep.xml test-data/2_mol.sdf test-data/change_title_on_CID_3033.sdf test-data/filterd_by_name.sdf test-data/molecule.fs test-data/ob_convert_on_CID2244.sdf test-data/ob_filter_on_CID2244.sdf test-data/ob_genprop_on_CID2244.sdf test-data/ob_remove_protonation_state.sdf |
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added:
__pycache__/cheminfolib.cpython-36.pyc |
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| diff -r 985ab0acd514 -r 64e2c5ab51cb __pycache__/cheminfolib.cpython-36.pyc |
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| Binary file __pycache__/cheminfolib.cpython-36.pyc has changed |
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| diff -r 985ab0acd514 -r 64e2c5ab51cb distance_finder.py --- a/distance_finder.py Thu Aug 15 11:05:06 2024 +0000 +++ b/distance_finder.py Thu Feb 19 15:09:27 2026 +0000 |
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| @@ -93,8 +93,6 @@ def main(): - global work_dir - parser = argparse.ArgumentParser( description="XChem distances - measure distances to particular points" ) |
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| diff -r 985ab0acd514 -r 64e2c5ab51cb ob_grep.xml --- a/ob_grep.xml Thu Aug 15 11:05:06 2024 +0000 +++ b/ob_grep.xml Thu Feb 19 15:09:27 2026 +0000 |
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| @@ -3,7 +3,7 @@ <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism--> <macros> <import>macros.xml</import> - <token name="@GALAXY_VERSION@">1</token> + <token name="@GALAXY_VERSION@">2</token> </macros> <options sanitize="False"/> <expand macro="requirements"/> @@ -47,10 +47,10 @@ <option value="multi">Upload one or more SMARTS patterns in a text file</option> </param> <when value="single"> - <param name="smarts_pattern" type="text" format="text" label="SMARTS Pattern" help="Specify a SMARTS Pattern for your search."/> + <param name="smarts_pattern" type="text" label="SMARTS Pattern" help="Specify a SMARTS Pattern for your search."/> </when> <when value="multi"> - <param name="query" type='data' format="tabular,text" label="Query file" help="One SMARTS pattern in each line."/> + <param name="query" type='data' format="tabular,txt" label="Query file" help="One SMARTS pattern in each line."/> </when> </conditional> <param name="invert_matches" type="boolean" label="Perform an inverted search, i.e. print non-matching molecules" truevalue="-v" falsevalue="" checked="false" /> @@ -66,8 +66,10 @@ <tests> <test> <param name="infile" ftype="smi" value="8_mol.smi"/> - <param name="inp" value="single"/> - <param name="smarts_pattern" value="CO"/> + <conditional name="input_type"> + <param name="inp" value="single"/> + <param name="smarts_pattern" value="CO"/> + </conditional> <param name="invert_matches" value="False" /> <param name="only_name" value="False" /> <param name="full_match" value="False" /> @@ -76,8 +78,10 @@ </test> <test> <param name="infile" ftype="smi" value="2_mol.smi"/> - <param name="inp" value="multi"/> - <param name="query" value="pattern.smarts" /> + <conditional name="input_type"> + <param name="inp" value="multi"/> + <param name="query" value="pattern.smarts" /> + </conditional> <output name="outfile" ftype="smi" file="ob_multi_obgrep.smi" /> </test> </tests> |
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| diff -r 985ab0acd514 -r 64e2c5ab51cb test-data/2_mol.sdf --- a/test-data/2_mol.sdf Thu Aug 15 11:05:06 2024 +0000 +++ b/test-data/2_mol.sdf Thu Feb 19 15:09:27 2026 +0000 |
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| @@ -1,5 +1,5 @@ CC(=O)Oc1ccccc1C(=O)[O-] InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)/p-1 - OpenBabel08132415422D + OpenBabel01232615512D 13 13 0 0 0 0 0 0 0 0999 V2000 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 @@ -32,7 +32,7 @@ M END $$$$ CC(=O)Oc1ccccc1C(=O)[O-] InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)/p-1 - OpenBabel08132415422D + OpenBabel01232615512D 13 13 0 0 0 0 0 0 0 0999 V2000 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 |
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| diff -r 985ab0acd514 -r 64e2c5ab51cb test-data/change_title_on_CID_3033.sdf --- a/test-data/change_title_on_CID_3033.sdf Thu Aug 15 11:05:06 2024 +0000 +++ b/test-data/change_title_on_CID_3033.sdf Thu Feb 19 15:09:27 2026 +0000 |
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| @@ -1,5 +1,5 @@ 214.7 - OpenBabel06291213403D + OpenBabel01232615513D 30 31 0 0 0 0 0 0 0 0999 V2000 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0 |
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| diff -r 985ab0acd514 -r 64e2c5ab51cb test-data/filterd_by_name.sdf --- a/test-data/filterd_by_name.sdf Thu Aug 15 11:05:06 2024 +0000 +++ b/test-data/filterd_by_name.sdf Thu Feb 19 15:09:27 2026 +0000 |
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| @@ -1,5 +1,5 @@ abc_one - OpenBabel03212013422D + OpenBabel01232615512D 26 30 0 0 0 0 0 0 0 0999 V2000 -8.6396 0.9568 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 @@ -67,7 +67,7 @@ $$$$ abc_eleven - OpenBabel03212013422D + OpenBabel01232615512D 32 35 0 0 1 0 0 0 0 0999 V2000 7.1381 -2.1568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 |
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| diff -r 985ab0acd514 -r 64e2c5ab51cb test-data/molecule.fs |
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| Binary file test-data/molecule.fs has changed |
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| diff -r 985ab0acd514 -r 64e2c5ab51cb test-data/ob_convert_on_CID2244.sdf --- a/test-data/ob_convert_on_CID2244.sdf Thu Aug 15 11:05:06 2024 +0000 +++ b/test-data/ob_convert_on_CID2244.sdf Thu Feb 19 15:09:27 2026 +0000 |
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| @@ -1,5 +1,5 @@ 2244 - OpenBabel03291606592D + OpenBabel01232615502D 21 21 0 0 0 0 0 0 0 0999 V2000 3.7320 -0.0600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 |
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| diff -r 985ab0acd514 -r 64e2c5ab51cb test-data/ob_filter_on_CID2244.sdf --- a/test-data/ob_filter_on_CID2244.sdf Thu Aug 15 11:05:06 2024 +0000 +++ b/test-data/ob_filter_on_CID2244.sdf Thu Feb 19 15:09:27 2026 +0000 |
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| @@ -1,5 +1,5 @@ 2244 - OpenBabel07101213142D + OpenBabel01232615522D 21 21 0 0 0 0 0 0 0 0999 V2000 3.7320 -0.0600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 |
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| diff -r 985ab0acd514 -r 64e2c5ab51cb test-data/ob_genprop_on_CID2244.sdf --- a/test-data/ob_genprop_on_CID2244.sdf Thu Aug 15 11:05:06 2024 +0000 +++ b/test-data/ob_genprop_on_CID2244.sdf Thu Feb 19 15:09:27 2026 +0000 |
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| @@ -1,5 +1,5 @@ 2244 - OpenBabel05191718512D + OpenBabel01232615482D 21 21 0 0 0 0 0 0 0 0999 V2000 3.7320 -0.0600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 |
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| diff -r 985ab0acd514 -r 64e2c5ab51cb test-data/ob_remove_protonation_state.sdf --- a/test-data/ob_remove_protonation_state.sdf Thu Aug 15 11:05:06 2024 +0000 +++ b/test-data/ob_remove_protonation_state.sdf Thu Feb 19 15:09:27 2026 +0000 |
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| @@ -1,5 +1,5 @@ 2244 - OpenBabel03291607022D + OpenBabel01232615542D 21 21 0 0 0 0 0 0 0 0999 V2000 3.7320 -0.0600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 |