# HG changeset patch # User bgruening # Date 1370500467 14400 # Node ID 9f25296ac1339c7657aec22aea4313dfdd3df730 # Parent 6db18ec30d4c8c16971c060e1edf9142482254c5 Deleted selected files diff -r 6db18ec30d4c -r 9f25296ac133 osra.py --- a/osra.py Thu Jun 06 02:33:42 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ -#!usr/bin/env python - -import os, sys -import subprocess - -""" - OSRA_DATA_FILES is set during the toolshed Installation - If it is not set, use the standard configuration of OSRA. - That means we need to delete argument 4-7. - That script is a hack, because we do not know the content of OSRA_DATA_FILES at xml evaluation time. - - osra -f $oformat $infile - -l \$OSRA_DATA_FILES/spelling.txt -a \$OSRA_DATA_FILES/superatom.txt - > $outfile -""" - -if not os.path.exists(sys.argv[6]): - # OSRA_DATA_FILES path is not set or the spelling file is not existent - sys.argv.pop(7) # superatom.txt path - sys.argv.pop(6) # -a - sys.argv.pop(5) # speling.txt path - sys.argv.pop(4) # -l - -subprocess.call(sys.argv[1:], stdout=sys.stdout) - - diff -r 6db18ec30d4c -r 9f25296ac133 osra.xml --- a/osra.xml Thu Jun 06 02:33:42 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ - - in Images or PDF documents (OSRA) - - osra - - - ## OSRA_DATA_FILES is set during the toolshed Installation - ## if it is not set, use the standard configuration and hope the best - osra.py -f $oformat $infile - -l \$OSRA_DATA_FILES/spelling.txt -a \$OSRA_DATA_FILES/superatom.txt - - ## further additions of OSRA parameter should go after -l and -a - ## because -l and -a can be removed by the python wrapper - - > $outfile - - - - - - - - - - - - - - - - - - - - - - - - -**What it does** - -OSRA detects molecules in images and converts them to standard molecule formats. - - - - diff -r 6db18ec30d4c -r 9f25296ac133 readme --- a/readme Thu Jun 06 02:33:42 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ -OSRA: Optical Structure Recognition Application - -OSRA is a utility designed to convert graphical representations of chemical -structures, as they appear in journal articles, patent documents, textbooks, -trade magazines etc., into SMILES (Simplified Molecular Input Line Entry -Specification - see http://en.wikipedia.org/wiki/SMILES) or -SD files - a computer recognizable molecular structure format. -OSRA can read a document in any of the over 90 graphical formats parseable by -ImageMagick - including GIF, JPEG, PNG, TIFF, PDF, PS etc., and generate -the SMILES or SDF representation of the molecular structure images encountered -within that document. - -Note that any software designed for optical recognition is unlikely to be -perfect, and the output produced might, and probably will, contain errors, -so curation by a human knowledgeable in chemical structures is highly recommended. - -http://cactus.nci.nih.gov/osra/ - -The wrapper comes with an automatic installation of all dependencies through the -galaxy toolshed. diff -r 6db18ec30d4c -r 9f25296ac133 repository_dependencies.xml --- a/repository_dependencies.xml Thu Jun 06 02:33:42 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ - - - - diff -r 6db18ec30d4c -r 9f25296ac133 test_data/CID_2244.png Binary file test_data/CID_2244.png has changed diff -r 6db18ec30d4c -r 9f25296ac133 test_data/CID_2244.sdf --- a/test_data/CID_2244.sdf Thu Jun 06 02:33:42 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,155 +0,0 @@ -2244 - -OEChem-05151212332D - - 21 21 0 0 0 0 0 0 0999 V2000 - 3.7320 -0.0600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 6.3301 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 4.5981 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 2.8660 -1.5600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 4.5981 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 5.4641 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 4.5981 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.3301 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 5.4641 -2.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.3301 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 5.4641 0.9400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2.8660 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2.0000 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 4.0611 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 6.8671 -0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 5.4641 -2.6800 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 6.8671 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 2.3100 0.4769 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 1.4631 0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 1.6900 -0.5969 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 6.3301 2.0600 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 1 5 1 0 0 0 0 - 1 12 1 0 0 0 0 - 2 11 1 0 0 0 0 - 2 21 1 0 0 0 0 - 3 11 2 0 0 0 0 - 4 12 2 0 0 0 0 - 5 6 1 0 0 0 0 - 5 7 2 0 0 0 0 - 6 8 2 0 0 0 0 - 6 11 1 0 0 0 0 - 7 9 1 0 0 0 0 - 7 14 1 0 0 0 0 - 8 10 1 0 0 0 0 - 8 15 1 0 0 0 0 - 9 10 2 0 0 0 0 - 9 16 1 0 0 0 0 - 10 17 1 0 0 0 0 - 12 13 1 0 0 0 0 - 13 18 1 0 0 0 0 - 13 19 1 0 0 0 0 - 13 20 1 0 0 0 0 -M END -> -2244 - -> -1 - -> -212 - -> -4 - -> -1 - -> -3 - -> -AAADccBwOAAAAAAAAAAAAAAAAAAAAAAAAAAwAAAAAAAAAAABAAAAGgAACAAADASAmAAyDoAABgCIAiDSCAACCAAkIAAIiAEGCMgMJzaENRqCe2Cl4BEIuYeIyCCOAAAAAAAIAAAAAAAAABAAAAAAAAAAAA== - -> -2-acetoxybenzoic acid - -> -2-acetyloxybenzoic acid - -> -2-acetyloxybenzoic acid - -> -2-acetyloxybenzoic acid - -> -2-acetoxybenzoic acid - -> -InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12) - -> -BSYNRYMUTXBXSQ-UHFFFAOYSA-N - -> -1.2 - -> -180.042259 - -> -C9H8O4 - -> -180.15742 - -> -CC(=O)OC1=CC=CC=C1C(=O)O - -> -CC(=O)OC1=CC=CC=C1C(=O)O - -> -63.6 - -> -180.042259 - -> -0 - -> -13 - -> -0 - -> -0 - -> -0 - -> -0 - -> -0 - -> -1 - -> -1 - -> -1 -5 -255 - -> -5 6 8 -5 7 8 -6 8 8 -7 9 8 -8 10 8 -9 10 8 - -$$$$ - diff -r 6db18ec30d4c -r 9f25296ac133 tool_dependencies.xml --- a/tool_dependencies.xml Thu Jun 06 02:33:42 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ - - - - - - http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.10.1.zip - - ../FastQC - $INSTALL_DIR/fastqc_dist - - chmod ugo+x $INSTALL_DIR/fastqc_dist/fastqc - - $INSTALL_DIR/fastqc_dist - - - - -