| Previous changeset 1:e2f40a02f31a (2019-06-04) Next changeset 3:cc0f89287ecf (2020-07-28) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 7efc367809c29ff5939ea971bd00c69b7f9f5903" |
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modified:
mordred_descriptors.py mordred_descriptors.xml test-data/10sdf.tab test-data/8smi.tab |
| b |
| diff -r e2f40a02f31a -r d074b0c2b54f mordred_descriptors.py --- a/mordred_descriptors.py Tue Jun 04 10:29:10 2019 -0400 +++ b/mordred_descriptors.py Wed Nov 06 13:59:30 2019 -0500 |
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| @@ -35,7 +35,7 @@ return [Chem.inchi.MolFromInchi(mol, sanitize=True) for mol in mols if mol != ''] -def mordred_descriptors(mols, output, header, use_3d): +def mordred_descriptors(mols, output, header, use_3d, smi_as_col): """ Calculate Mordred descriptors and save as tabular """ @@ -47,6 +47,10 @@ df.iloc[mol] = np.nan df = df.applymap(convert_errors_to_nan) # remove descriptors which errored df = df.round(6) + if smi_as_col: + smiles = [Chem.MolToSmiles(mol) for mol in mols] + df['SMILES'] = smiles + df.to_csv(output, na_rep='', sep='\t', index=False, header=header) # write output @@ -65,7 +69,11 @@ parser.add_argument("--header", dest="header", action="store_true", default=False, help="Write header line.") + + parser.add_argument("--smiles", dest="smiles", action="store_true", + default=False, + help="Add a column with compound SMILES.") args = parser.parse_args() mols = mol_supplier(args.infile, args.iformat) - mordred_descriptors(mols, args.outfile, args.header, args.use_3d) + mordred_descriptors(mols, args.outfile, args.header, args.use_3d, args.smiles) |
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| diff -r e2f40a02f31a -r d074b0c2b54f mordred_descriptors.xml --- a/mordred_descriptors.xml Tue Jun 04 10:29:10 2019 -0400 +++ b/mordred_descriptors.xml Wed Nov 06 13:59:30 2019 -0500 |
| [ |
| @@ -1,7 +1,7 @@ -<tool id="ctb_mordred_descriptors" name="Calculate molecular descriptors" version="0.1.0"> +<tool id="ctb_mordred_descriptors" name="Calculate molecular descriptors" version="1.2.0"> <description>with Mordred</description> <requirements> - <requirement type="package" version="1.1.2">mordred</requirement> + <requirement type="package" version="1.2.0">mordred</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/mordred_descriptors.py' @@ -10,6 +10,7 @@ -o '${output}' $header $use_3d + $smi_col ]]></command> <inputs> <param name="input" format="smi,sdf,inchi" type="data" label="Molecule data" @@ -18,6 +19,8 @@ label='Include a header line' help='Include names of the descriptors as the first line in the output file'/> <param name='use_3d' type='boolean' truevalue='--3d' falsevalue='' label='Calculate 3D descriptors' help='Include 3D as well as 2D descriptors - only valid if an SD-file is selected'/> + <param name='smi_col' type='boolean' truevalue='--smiles' falsevalue='' + label='Add column with SMILES' help='Add a column to the output file containing SMILES of all compounds'/> </inputs> <outputs> <data name="output" format="tabular" /> @@ -27,12 +30,14 @@ <param name="input" ftype='sdf' value="10mol.sdf" /> <param name="header" value="True" /> <param name="use_3d" value="True" /> + <param name="smi_col" value="False" /> <output name="output" ftype='tabular' file="10sdf.tab" /> </test> <test> <param name="input" ftype='smi' value="8mol.smi" /> <param name="header" value="True" /> <param name="use_3d" value="False" /> + <param name="smi_col" value="True" /> <output name="output" ftype='tabular' file="8smi.tab" /> </test> </tests> |
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| diff -r e2f40a02f31a -r d074b0c2b54f test-data/10sdf.tab --- a/test-data/10sdf.tab Tue Jun 04 10:29:10 2019 -0400 +++ b/test-data/10sdf.tab Wed Nov 06 13:59:30 2019 -0500 |
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| b'@@ -1,11 +1,11 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|
| b |
| diff -r e2f40a02f31a -r d074b0c2b54f test-data/8smi.tab --- a/test-data/8smi.tab Tue Jun 04 10:29:10 2019 -0400 +++ b/test-data/8smi.tab Wed Nov 06 13:59:30 2019 -0500 |
| [ |
| b'@@ -1,9 +1,9 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