Mercurial > repos > bgruening > ctb_im_xcos
changeset 1:9b6210854c8c draft default tip
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit d1d0ec4ebc97b2274b18a0aab99f41addd5357ae"
| author | bgruening |
|---|---|
| date | Mon, 27 Jul 2020 11:30:49 -0400 |
| parents | 73164cea9b60 |
| children | |
| files | macros.xml test-data/poses.sdf xcos.xml |
| diffstat | 3 files changed, 19 insertions(+), 17 deletions(-) [+] |
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--- a/macros.xml Tue Jul 21 05:22:23 2020 -0400 +++ b/macros.xml Mon Jul 27 11:30:49 2020 -0400 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">1.1.3</token> + <token name="@TOOL_VERSION@">1.1.4</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">im-pipelines</requirement> @@ -7,7 +7,7 @@ </xml> <xml name="input"> - <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF or JSON format"/> + <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/> </xml> <xml name="outputs" token_output_format="sdf" token_filetype="sdf"> @@ -21,16 +21,16 @@ <citations> <citation type="bibtex"> @article{rdkit, - author = {Greg Landrum and others}, - title = {RDKit: Open-source cheminformatics}, - url = {http://www.rdkit.org} - }</citation> + author = {Greg Landrum and others}, + title = {RDKit: Open-source cheminformatics}, + url = {http://www.rdkit.org} + }</citation> <citation type="bibtex"> @article{im-pipelines, - author = {Tim Dudgeon and others}, - title = {InformaticsMatters pipeline components for cheminformatics and computational chemistry.}, - url = {https://github.com/InformaticsMatters/pipelines} - }</citation> + author = {Tim Dudgeon and others}, + title = {InformaticsMatters pipeline components for cheminformatics and computational chemistry.}, + url = {https://github.com/InformaticsMatters/pipelines} + }</citation> <yield /> </citations> </xml>
--- a/test-data/poses.sdf Tue Jul 21 05:22:23 2020 -0400 +++ b/test-data/poses.sdf Mon Jul 27 11:30:49 2020 -0400 @@ -961,4 +961,4 @@ > <TETHERED ATOMS> (14) 1,2,3,4,5,6,7,8,9,10,11,15,16 -$$$$ +$$$$ \ No newline at end of file
--- a/xcos.xml Tue Jul 21 05:22:23 2020 -0400 +++ b/xcos.xml Mon Jul 27 11:30:49 2020 -0400 @@ -31,8 +31,10 @@ <param name="fragments" ftype='sdf' value="hits-17.sdf" /> <output name="output" ftype='sdf'> <assert_contents> - <has_text text="XCos_Score3" /> - <has_n_lines n="818" /> + <has_text text="XCos_RefMols" /> + <has_text text="XCos_NumHits" /> + <has_text text="XCos_Score1" /> + <has_n_lines n="734" /> </assert_contents> </output> </test> @@ -49,12 +51,12 @@ The molecule is fragmented using the BRICS algorithm and each fragment (bit) is compared to the ligands using the SuCOS methodology. The resulting scores are the combined scores of the bits. -XCoseScore1 - -XCoseScore2 - -XCoseScore3 - +XCos_RefMols - The fragments that the ligand overlays +XCos_NumHits - the number of fragments the ligand overlays +XCos_Score1 - The sum of each bit's feature and shape overlay score scaled by the number of heavy bit atoms. XCos was conceived and implemented by Warren Thompson <warren.thompson@diamond.ac.uk>. -The original code can be found here: https://github.com/Waztom/xchem-notebooks/blob/master/XCOS.ipynb +The original code can be found here: https://github.com/Waztom/xchem-XCOS -----