Mercurial > repos > bgruening > osra
changeset 11:143a63ca2bca
Uploaded
| author | bgruening |
|---|---|
| date | Thu, 23 May 2013 16:19:16 -0400 |
| parents | dcbe4666c052 |
| children | f265bcf0ddc5 |
| files | osra.py osra.xml repository_dependencies.xml test_data/2008001635_153_chem.png test_data/2008001635_153_chem.smi tool_dependencies.xml |
| diffstat | 6 files changed, 43 insertions(+), 23 deletions(-) [+] |
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--- a/osra.py Thu May 23 02:57:31 2013 -0400 +++ b/osra.py Thu May 23 16:19:16 2013 -0400 @@ -14,13 +14,14 @@ > $outfile """ -if not os.path.exists(sys.argv[6]): +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 -subprocess.call(sys.argv[1:], stdout=sys.stdout) +sys.argv[0] = 'osra' +subprocess.call(sys.argv, stdout=sys.stdout)
--- a/osra.xml Thu May 23 02:57:31 2013 -0400 +++ b/osra.xml Thu May 23 16:19:16 2013 -0400 @@ -1,7 +1,7 @@ -<tool id="osra" name="Molecule recognition" version="0.2"> +<tool id="osra" name="Molecule recognition" version="0.3"> <description>in Images or PDF documents (OSRA)</description> <requirements> - <requirement type="package" version="1.4.0">osra</requirement> + <requirement type="package" version="2.0.0">osra</requirement> </requirements> <command interpreter='python'> ## OSRA_DATA_FILES is set during the toolshed Installation @@ -12,6 +12,10 @@ ## further additions of OSRA parameter should go after -l and -a ## because -l and -a can be removed by the python wrapper + $confidence + $adaptive + $thinning + > $outfile </command> <inputs> @@ -20,6 +24,10 @@ <option value="can">SMILES</option> <option value="sdf">SDF</option> </param> + <param name="confidence" type="boolean" label="Print out confidence estimate (-p)" truevalue="-p" falsevalue="" checked="true" /> + <param name="adaptive" type="boolean" label="Adaptive thresholding pre-processing, useful for low light/low contrast images (-i)" truevalue="-i" falsevalue="" checked="false" /> + <param name="thinning" type="boolean" label="Additional thinning/scaling down of low quality documents (-j)" truevalue="-j" falsevalue="" checked="false" /> + </inputs> <outputs> <data name="outfile" type="data" format="sdf"> @@ -34,6 +42,12 @@ <param name="oformat" value="sdf"/> <output name="outfile" ftype="sdf" file="osra_on_CID2244.sdf"/> </test> + <test> + <param name="infile" ftype="png" value="2008001635_153_chem.png"/> + <param name="oformat" value="can"/> + <output name="outfile" ftype="sdf" file="2008001635_153_chem.smi"/> + </test> + </tests> <help>
--- a/repository_dependencies.xml Thu May 23 02:57:31 2013 -0400 +++ b/repository_dependencies.xml Thu May 23 16:19:16 2013 -0400 @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format)."> <repository changeset_revision="1b63345907ec" name="molecule_datatypes" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" /> -</repositories> \ No newline at end of file +</repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test_data/2008001635_153_chem.smi Thu May 23 16:19:16 2013 -0400 @@ -0,0 +1,1 @@ +CCC(c1ccc(cc1)Br)OCCCO
--- a/tool_dependencies.xml Thu May 23 02:57:31 2013 -0400 +++ b/tool_dependencies.xml Thu May 23 16:19:16 2013 -0400 @@ -6,13 +6,13 @@ <package name="graphicsmagick" version="1.3.18"> <repository changeset_revision="34f511310435" name="package_graphicsmagick_1_3" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="osra" version="1.4.0"> + <package name="osra" version="2.0.0"> <install version="1.0"> <actions> - - <action type="download_by_url">http://downloads.sourceforge.net/project/osra/osra/1.4.0/osra-1.4.0.tgz</action> + <!-- first action is always downloading --> + <action type="download_by_url">http://downloads.sourceforge.net/project/osra/osra/2.0.0/osra-2.0.0.tgz</action> - + <!-- populate the environment variables from the dependend repos --> <action type="set_environment_for_install"> <repository changeset_revision="efffcee80e03" name="package_openbabel_2_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu"> <package name="openbabel" version="2.3.2" /> @@ -22,49 +22,53 @@ </repository> </action> - + <!--compiling potrace-1.11 --> <action type="shell_command">wget http://potrace.sourceforge.net/download/potrace-1.11.tar.gz</action> <action type="shell_command">tar xfvz potrace-1.11.tar.gz && cd potrace-1.11 && ./configure --with-libpotrace --prefix=$INSTALL_DIR/potrace/build && make && make install</action> - + <!--compiling gocr 0.50patched --> + <!-- not yet possible + <action type="shell_command">wget http://www-e.uni-magdeburg.de/jschulen/ocr/gocr-0.50.tar.gz</action> + <action type="shell_command">tar xfvz gocr-0.50.tar.gz && cd gocr-0.50 && ./configure -|-prefix=$INSTALL_DIR/gocr/build && make libs && make all install</action> + --> <action type="shell_command">wget http://downloads.sourceforge.net/project/osra/gocr-patched/gocr-0.50pre-patched.tgz</action> <action type="shell_command">tar xfvz gocr-0.50pre-patched.tgz && cd gocr-0.50pre-patched && ./configure --prefix=$INSTALL_DIR/gocr/build && make libs && make all install</action> - + + <!--compiling tclap 1.2.1 --> <action type="shell_command">wget http://downloads.sourceforge.net/project/tclap/tclap-1.2.1.tar.gz</action> <action type="shell_command">tar xfvz tclap-1.2.1.tar.gz && cd tclap-1.2.1 && ./configure --prefix=$INSTALL_DIR/tclap/build && make && make install</action> - + <!--compiling ocrad 0.21 --> <action type="shell_command">wget http://mirror.checkdomain.de/gnu/ocrad/ocrad-0.21.tar.gz</action> <action type="shell_command">tar xfvz ocrad-0.21.tar.gz && cd ocrad-0.21 && ./configure --prefix=$INSTALL_DIR/ocrad/build && make && make install</action> - + <!--compiling cuneiform 1.1.0 --> <action type="shell_command">wget https://launchpad.net/cuneiform-linux/1.1/1.1/+download/cuneiform-linux-1.1.0.tar.bz2</action> <action type="shell_command">tar xfvj cuneiform-linux-1.1.0.tar.bz2 && cd cuneiform-linux-1.1.0 && mkdir build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/cuneiform/build/ && make && make install</action> - - <action type="shell_command">wget http://share.gruenings.eu/osra-1.4.0-configure.patch</action> - <action type="shell_command">patch configure < osra-1.4.0-configure.patch</action> - - <action type="shell_command">export PATH=$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=$INSTALL_DIR/cuneiform/build/install/include/ --with-cuneiform --with-cuneiform-lib=$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=$INSTALL_DIR </action> + <!--And finally OSRA 1.4.0--> + <!-- Extending the PATH is needed for OSRA --> + <action type="shell_command">export PATH=$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=$INSTALL_DIR/cuneiform/build/install/include/ --with-cuneiform --with-cuneiform-lib=$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 </action> <action type="shell_command">make</action> <action type="shell_command">make install</action> <action type="shell_command">rm $INSTALL_DIR/tclap/ -r</action> - + <!--<action type="shell_command">rm $INSTALL_DIR/openbabel/ -r</action>--> <action type="shell_command">rm $INSTALL_DIR/gocr/ -r</action> <action type="shell_command">rm $INSTALL_DIR/ocrad/ -r</action> <action type="shell_command">rm $INSTALL_DIR/cuneiform/ -r</action> <action type="set_environment"> - <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$GRAPHICSMAGICK_ROOT_DIR/lib/</environment_variable> + <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[$GRAPHICSMAGICK_ROOT_DIR]/lib/</environment_variable> <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/potrace/build/lib/</environment_variable> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - + <!-- OSRA_DATA_FILES is only used by the galaxy wrapper and is not part of OSRA --> <environment_variable action="set_to" name="OSRA_DATA_FILES">$INSTALL_DIR/share</environment_variable> </action> </actions> </install> <readme>We still have a handfull of requirements</readme> </package> -</tool_dependency> \ No newline at end of file +</tool_dependency>