# HG changeset patch
# User bgruening
# Date 1446392020 18000
# Node ID d323837e346dd462009b8d036acdc9d1f865d24c
# Parent 70b28a917515515887b4606b74bdf26d6d951a73
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
diff -r 70b28a917515 -r d323837e346d confab.tar.bz2
Binary file confab.tar.bz2 has changed
diff -r 70b28a917515 -r d323837e346d confab.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/confab.xml Sun Nov 01 10:33:40 2015 -0500
@@ -0,0 +1,142 @@
+
+ for molecules (confab)
+
+
+ confab
+
+
+&1
+]]>
+
+
+
+
+
+
+
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diff -r 70b28a917515 -r d323837e346d osra.py
--- a/osra.py Sun Nov 01 10:31:25 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +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[7]):
- # 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
-
-sys.argv[0] = 'osra'
-subprocess.call(sys.argv, stdout=sys.stdout)
-
-
diff -r 70b28a917515 -r d323837e346d osra.tar.bz2
Binary file osra.tar.bz2 has changed
diff -r 70b28a917515 -r d323837e346d osra.xml
--- a/osra.xml Sun Nov 01 10:31:25 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,78 +0,0 @@
-
- in Images or PDF documents (OSRA)
-
- osra
- openbabel
- graphicsmagick
-
-
- $outfile
-]]>
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
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-
-
-
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-
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-
-
-
diff -r 70b28a917515 -r d323837e346d readme
--- a/readme Sun Nov 01 10:31:25 2015 -0500
+++ /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 70b28a917515 -r d323837e346d test-data/CID_3033.sdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CID_3033.sdf Sun Nov 01 10:33:40 2015 -0500
@@ -0,0 +1,271 @@
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+$$$$
+
diff -r 70b28a917515 -r d323837e346d test-data/confab_on_CID3033.sdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/confab_on_CID3033.sdf Sun Nov 01 10:33:40 2015 -0500
@@ -0,0 +1,270 @@
+214.7
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diff -r 70b28a917515 -r d323837e346d test_data/2008001635_153_chem.png
Binary file test_data/2008001635_153_chem.png has changed
diff -r 70b28a917515 -r d323837e346d test_data/2008001635_153_chem.smi
--- a/test_data/2008001635_153_chem.smi Sun Nov 01 10:31:25 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-CCC(c1ccc(cc1)Br)OCCCO
diff -r 70b28a917515 -r d323837e346d test_data/CID_2244.png
Binary file test_data/CID_2244.png has changed
diff -r 70b28a917515 -r d323837e346d test_data/CID_2244.sdf
--- a/test_data/CID_2244.sdf Sun Nov 01 10:31:25 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,155 +0,0 @@
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-M END
->
-2244
-
->
-1
-
->
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-
->
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-
->
-1
-
->
-3
-
->
-AAADccBwOAAAAAAAAAAAAAAAAAAAAAAAAAAwAAAAAAAAAAABAAAAGgAACAAADASAmAAyDoAABgCIAiDSCAACCAAkIAAIiAEGCMgMJzaENRqCe2Cl4BEIuYeIyCCOAAAAAAAIAAAAAAAAABAAAAAAAAAAAA==
-
->
-2-acetoxybenzoic acid
-
->
-2-acetyloxybenzoic acid
-
->
-2-acetyloxybenzoic acid
-
->
-2-acetyloxybenzoic acid
-
->
-2-acetoxybenzoic acid
-
->
-InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)
-
->
-BSYNRYMUTXBXSQ-UHFFFAOYSA-N
-
->
-1.2
-
->
-180.042259
-
->
-C9H8O4
-
->
-180.15742
-
->
-CC(=O)OC1=CC=CC=C1C(=O)O
-
->
-CC(=O)OC1=CC=CC=C1C(=O)O
-
->
-63.6
-
->
-180.042259
-
->
-0
-
->
-13
-
->
-0
-
->
-0
-
->
-0
-
->
-0
-
->
-0
-
->
-1
-
->
-1
-
->
-1
-5
-255
-
->
-5 6 8
-5 7 8
-6 8 8
-7 9 8
-8 10 8
-9 10 8
-
-$$$$
-
diff -r 70b28a917515 -r d323837e346d tool_dependencies.xml
--- a/tool_dependencies.xml Sun Nov 01 10:31:25 2015 -0500
+++ b/tool_dependencies.xml Sun Nov 01 10:33:40 2015 -0500
@@ -1,74 +1,30 @@
-
-
+
+
-
-
-
-
+
-
- http://downloads.sourceforge.net/project/osra/osra/2.0.0/osra-2.0.0.tgz
+ https://github.com/bgruening/confab/archive/1.0.1.tar.gz
-
-
-
-
-
+
+
-
- http://potrace.sourceforge.net/download/1.11/potrace-1.11.tar.gz
- tar xfvz potrace-1.11.tar.gz && cd potrace-1.11 && ./configure --with-libpotrace --prefix=$INSTALL_DIR/potrace/build && make && make install
-
-
-
- http://downloads.sourceforge.net/project/osra/gocr-patched/gocr-0.50pre-patched.tgz
- tar xfvz gocr-0.50pre-patched.tgz && cd gocr-0.50pre-patched && ./configure --prefix=$INSTALL_DIR/gocr/build && make libs && make all install
-
-
-
- http://downloads.sourceforge.net/project/tclap/tclap-1.2.1.tar.gz
- tar xfvz tclap-1.2.1.tar.gz && cd tclap-1.2.1 && ./configure --prefix=$INSTALL_DIR/tclap/build && make && make install
-
-
- http://mirror.checkdomain.de/gnu/ocrad/ocrad-0.21.tar.gz
- tar xfvz ocrad-0.21.tar.gz && cd ocrad-0.21 && ./configure --prefix=$INSTALL_DIR/ocrad/build && make && make install
-
-
- https://launchpad.net/cuneiform-linux/1.1/1.1/+download/cuneiform-linux-1.1.0.tar.bz2
- tar xfvj cuneiform-linux-1.1.0.tar.bz2 && cd cuneiform-linux-1.1.0 && mkdir build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/cuneiform/build/ && make && make install
-
-
-
- export PATH=$PATH:$GRAPHICSMAGICK_ROOT_DIR/bin/ &&
- ./configure --with-tclap-include=$INSTALL_DIR/tclap/build/include/ --with-potrace-include=$INSTALL_DIR/potrace/build/include/ --with-potrace-lib=$INSTALL_DIR/potrace/build/lib/ --with-gocr-include=$INSTALL_DIR/gocr/build/include/gocr/ --with-gocr-lib=$INSTALL_DIR/gocr/build/lib/ --with-ocrad-include=$INSTALL_DIR/ocrad/build/include/ --with-ocrad-lib=$INSTALL_DIR/ocrad/build/lib/ --with-cuneiform-include=$INSTALL_DIR/cuneiform/build/include/ --with-cuneiform --with-cuneiform-lib=$INSTALL_DIR/cuneiform/build/install/lib/ --with-openbabel-include=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ --with-openbabel-lib=$OPENBABEL_LIB_DIR --with-graphicsmagick-lib=$GRAPHICSMAGICK_ROOT_DIR/lib/ --with-graphicsmagick-include=$GRAPHICSMAGICK_ROOT_DIR/include/GraphicsMagick/ --prefix=$INSTALL_DIR
+ cmake . -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR -DEIGEN2_INCLUDE_DIR=$EIGEN2_SOURCE_PATH
make
make install
-
- rm $INSTALL_DIR/tclap/ -r
-
- rm $INSTALL_DIR/gocr/ -r
- rm $INSTALL_DIR/ocrad/ -r
- rm $INSTALL_DIR/cuneiform/ -r
-
- $ENV[GRAPHICSMAGICK_ROOT_DIR]/lib/
- $INSTALL_DIR/potrace/build/lib/
$INSTALL_DIR/bin
-
- $INSTALL_DIR/share
+ $INSTALL_DIR/share/openbabel
+ $INSTALL_DIR/lib/openbabel/2.2.99
- We still have a handfull of requirements
+ Compiling Confab requires g++, CMake 2.4+. Optional but required for a few features is libxml2 and zlib.