Mercurial > repos > bgruening > osra

annotate readme.md @ 23:e41a468bc40d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:28:05 -0400
parents 6cafe4f5d181
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
22
6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
bgruening
parents:
diff changeset
1 ## OSRA: Optical Structure Recognition Application
6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
bgruening
parents:
diff changeset
2
6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
bgruening
parents:
diff changeset
3 OSRA is a utility designed to convert graphical representations of chemical
6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
bgruening
parents:
diff changeset
4 structures, as they appear in journal articles, patent documents, textbooks,
6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
bgruening
parents:
diff changeset
5 trade magazines etc., into SMILES (Simplified Molecular Input Line Entry
6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
bgruening
parents:
diff changeset
6 Specification - see http://en.wikipedia.org/wiki/SMILES) or
6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
bgruening
parents:
diff changeset
7 SD files - a computer recognizable molecular structure format.
6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
bgruening
parents:
diff changeset
8 OSRA can read a document in any of the over 90 graphical formats parseable by
6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
bgruening
parents:
diff changeset
9 ImageMagick - including GIF, JPEG, PNG, TIFF, PDF, PS etc., and generate
6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
bgruening
parents:
diff changeset
10 the SMILES or SDF representation of the molecular structure images encountered
6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
bgruening
parents:
diff changeset
11 within that document.
6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
bgruening
parents:
diff changeset
12
6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
bgruening
parents:
diff changeset
13 Note that any software designed for optical recognition is unlikely to be
6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
bgruening
parents:
diff changeset
14 perfect, and the output produced might, and probably will, contain errors,
6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
bgruening
parents:
diff changeset
15 so curation by a human knowledgeable in chemical structures is highly recommended.
6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
bgruening
parents:
diff changeset
16
6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
bgruening
parents:
diff changeset
17 http://cactus.nci.nih.gov/osra/
6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
bgruening
parents:
diff changeset
18
6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
bgruening
parents:
diff changeset
19 The wrapper comes with an automatic installation of all dependencies through the
6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
bgruening
parents:
diff changeset
20 galaxy toolshed.