| Previous changeset 8:d00ae56d3ba5 (2019-05-10) Next changeset 10:e6011617c748 (2020-03-25) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit a889b6ed75666406a95e29d672b58a8fee6e8784" |
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modified:
macros.xml ob_convert.xml |
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added:
test-data/split1.pdbqt test-data/split2.pdbqt |
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| diff -r d00ae56d3ba5 -r a072cb207571 macros.xml --- a/macros.xml Fri May 10 08:53:48 2019 -0400 +++ b/macros.xml Thu Aug 22 10:30:36 2019 -0400 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION@">2.4.2</token> + <token name="@VERSION@">2.4.2.1</token> <xml name="requirements"> <requirements> |
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| diff -r d00ae56d3ba5 -r a072cb207571 ob_convert.xml --- a/ob_convert.xml Fri May 10 08:53:48 2019 -0400 +++ b/ob_convert.xml Thu Aug 22 10:30:36 2019 -0400 |
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| @@ -13,28 +13,37 @@ #set $format = $oformat.oformat_opts_selector - #if $format == "fs": + #if $format == 'fs': ## For the fastsearch index we need to copy the original molecule files to the composite datatype of obfs. ## Because openbabel likes file extensions, we give the molecule file a proper file extension. mkdir $outfile.files_path; - cp "${infile}" ${os.path.join($outfile.files_path, 'molecule.%s' % $infile.ext )}; + cp '${infile}' ${os.path.join($outfile.files_path, 'molecule.%s' % $infile.ext )}; + #end if + + #if $split == 'true': + mkdir output && #end if - obabel -i "${infile.ext}" + obabel -i '${infile.ext}' - #if $format == "fs": + #if $format == 'fs': ## the fs filetype need his own symlink path, all others can take the original ones ${os.path.join($outfile.files_path, 'molecule.%s' % $infile.ext )} - -o "$format" -e + -o '$format' -e -O ${os.path.join($outfile.files_path,'molecule.fs')} #if int($oformat.fs_fold) > 0: -xN$oformat.fs_fold #end if ${oformat.fs_fptype} #else: - "${infile}" - -o "${format}" - -O "${outfile}" + '${infile}' + -o '${format}' + #if $split == 'true': + -O 'output/molecule.$format' + -m + #else: + -O '${outfile}' + #end if -e #end if @@ -188,6 +197,7 @@ <option value="nw">NWChem input format</option> <option value="pcm">PCModel format</option> <option value="pdb">Protein Data Bank format (pdb)</option> + <option value="pdbqt">PDBQT input format</option> <option value="pov">POV-Ray input format</option> <option value="pqs">Parallel Quantum Solutions format</option> <option value="qcin">Q-Chem input format</option> @@ -335,6 +345,7 @@ <when value="nw" /> <when value="pcm" /> <when value="pdb" /> + <when value="pdbqt" /> <when value="pov" /> <when value="pqs" /> <when value="qcin" /> @@ -379,6 +390,7 @@ </conditional> <!-- Options for all formats.--> + <param name="split" type="boolean" value="false" label="Split multi-molecule files into a collection"/> <param name="remove_h" type="boolean" truevalue="-d" falsevalue="" label="Delete hydrogen atoms, make all hydrogens implicit" help="(-d)" /> <param name="ph" type="float" value="-1" label="Add hydrogens appropriate for pH" help="-1 means deactivated (-p)"/> @@ -415,6 +427,7 @@ <outputs> <data name="outfile" format="text" label="Convert to ${oformat.oformat_opts_selector} from ${on_string}"> + <filter>split == False</filter> <change_format> <when input="oformat.oformat_opts_selector" value="sdf" format="sdf"/> <when input="oformat.oformat_opts_selector" value="can" format="smi"/> @@ -424,9 +437,15 @@ <when input="oformat.oformat_opts_selector" value="cml" format="cml"/> <when input="oformat.oformat_opts_selector" value="mol" format="mol"/> <when input="oformat.oformat_opts_selector" value="pdb" format="pdb"/> + <when input="oformat.oformat_opts_selector" value="pdbqt" format="pdbqt"/> <when input="oformat.oformat_opts_selector" value="fs" format="obfs"/> </change_format> </data> + + <collection name="file_outputs" type="list" label="Prepared ligands" > + <filter>split == True</filter> + <discover_datasets pattern="__name_and_ext__" directory="output" visible="false" /> + </collection> </outputs> <tests> <test> @@ -462,6 +481,15 @@ <param name="oformat_opts_selector" value="sdf" /> <output name="outfile" ftype="sdf" file="ob_convert_on_CID2244.sdf" lines_diff="2"/> </test> + <test> + <param name="infile" ftype="smi" value="2_mol.smi"/> + <param name="oformat_opts_selector" value="pdbqt"/> + <param name="split" value="true"/> + <output_collection name="file_outputs" type="list" count="2"> + <element name="molecule1" file="split1.pdbqt" /> + <element name="molecule2" file="split2.pdbqt" /> + </output_collection> + </test> </tests> <help> <![CDATA[ |
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| diff -r d00ae56d3ba5 -r a072cb207571 test-data/split1.pdbqt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/split1.pdbqt Thu Aug 22 10:30:36 2019 -0400 |
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| @@ -0,0 +1,30 @@ +REMARK Name = +REMARK 3 active torsions: +REMARK status: ('A' for Active; 'I' for Inactive) +REMARK 1 A between atoms: C_2 and O_4 +REMARK 2 A between atoms: O_4 and C_5 +REMARK 3 A between atoms: C_10 and C_11 +REMARK x y z vdW Elec q Type +REMARK _______ _______ _______ _____ _____ ______ ____ +ROOT +ATOM 1 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.149 A +ATOM 2 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.038 A +ATOM 3 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.003 A +ATOM 4 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 A +ATOM 5 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.004 A +ATOM 6 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.049 A +ENDROOT +BRANCH 6 7 +ATOM 7 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.076 C +ATOM 8 O UNL 1 0.000 0.000 0.000 0.00 0.00 -0.544 OA +ATOM 9 O UNL 1 0.000 0.000 0.000 0.00 0.00 -0.544 OA +ENDBRANCH 6 7 +BRANCH 1 10 +ATOM 10 O UNL 1 0.000 0.000 0.000 0.00 0.00 -0.424 OA +BRANCH 10 12 +ATOM 11 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.122 C +ATOM 12 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.322 C +ATOM 13 O UNL 1 0.000 0.000 0.000 0.00 0.00 -0.250 OA +ENDBRANCH 10 12 +ENDBRANCH 1 10 +TORSDOF 3 |
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| diff -r d00ae56d3ba5 -r a072cb207571 test-data/split2.pdbqt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/split2.pdbqt Thu Aug 22 10:30:36 2019 -0400 |
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| @@ -0,0 +1,30 @@ +REMARK Name = +REMARK 3 active torsions: +REMARK status: ('A' for Active; 'I' for Inactive) +REMARK 1 A between atoms: C_2 and O_4 +REMARK 2 A between atoms: O_4 and C_5 +REMARK 3 A between atoms: C_10 and C_11 +REMARK x y z vdW Elec q Type +REMARK _______ _______ _______ _____ _____ ______ ____ +ROOT +ATOM 1 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.149 A +ATOM 2 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.038 A +ATOM 3 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.003 A +ATOM 4 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 A +ATOM 5 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.004 A +ATOM 6 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.049 A +ENDROOT +BRANCH 6 7 +ATOM 7 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.076 C +ATOM 8 O UNL 1 0.000 0.000 0.000 0.00 0.00 -0.544 OA +ATOM 9 O UNL 1 0.000 0.000 0.000 0.00 0.00 -0.544 OA +ENDBRANCH 6 7 +BRANCH 1 10 +ATOM 10 O UNL 1 0.000 0.000 0.000 0.00 0.00 -0.424 OA +BRANCH 10 12 +ATOM 11 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.122 C +ATOM 12 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.322 C +ATOM 13 O UNL 1 0.000 0.000 0.000 0.00 0.00 -0.250 OA +ENDBRANCH 10 12 +ENDBRANCH 1 10 +TORSDOF 3 |