| Previous changeset 0:fc8d71a0fb9b (2017-05-22) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e |
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modified:
strip-it.xml |
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| diff -r fc8d71a0fb9b -r b8809b15e1a4 strip-it.xml --- a/strip-it.xml Mon May 22 03:01:21 2017 -0400 +++ b/strip-it.xml Tue May 07 13:42:01 2019 -0400 |
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| @@ -1,5 +1,5 @@ <tool id="ctb_stripit" name="Strip-it" version="1.0.2.1"> - <description>extracts predefined scaffolds from molecules</description> + <description>extracts scaffolds from molecules</description> <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="1000" shared_inputs="" merge_outputs="outfile"></parallelism--> <requirements> <requirement type="package" version="1.0.2">strip_it</requirement> @@ -38,11 +38,8 @@ **What this tool does** -Strip-it is a program that extracts predefined scaffolds from organic small -molecules. - -The program comes with a number of predefined molecular scaffolds for -extraction. These scaffolds include, amongst others +Strip-it is a program that extracts scaffolds from organic small molecules, +based on predefined scaffold types. The scaffold types used by Strip-it include - `molecular frameworks`_ as originally described by Bemis and Murcko - `molecular frameworks and the reduced molecular frameworks`_ as described by Ansgar Schuffenhauer and coworkers @@ -59,13 +56,13 @@ **Input** -| - `SD-Format`_ -| - `SMILES Format`_ -| - `MOL2 Format`_ +| - `SDF format`_ +| - `SMILES format`_ +| - `MOL2 format`_ -.. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file -.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification -.. _MOL2 Format: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf +.. _SDF format: http://en.wikipedia.org/wiki/Chemical_table_file +.. _SMILES format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification +.. _MOL2 format: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf ----- @@ -74,6 +71,9 @@ **Output** +A tabular file with the name and SMILES of the molecule in the first two +columns; subsequent columns show scaffolds extracted by different methods. + +-------------+--------------------------------+----------------------+------------------------+----------------------+-----+ | NAME | MOLECULE | RINGS_WITH_LINKERS_1 | RINGS_WITH_LINKERS_2 | MURCKO_1 | ... | +=============+================================+======================+========================+======================+=====+ @@ -98,5 +98,11 @@ ]]> </help> <citations> + <citation type="bibtex">@misc{ + title={Strip-it}, + author={Silicos-it}, + year={2014}, + + }</citation> </citations> </tool> |