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annotate readme.md @ 22:6cafe4f5d181 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
author bgruening
date Thu, 09 Nov 2017 03:41:26 -0500
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6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
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1 ## OSRA: Optical Structure Recognition Application
6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
bgruening
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6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
bgruening
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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
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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
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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
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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
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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
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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
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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
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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
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11 within that document.
6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
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6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
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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
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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
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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
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6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
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17 http://cactus.nci.nih.gov/osra/
6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
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6cafe4f5d181 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
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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
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20 galaxy toolshed.