Mercurial > repos > bgruening > osra
changeset 2:d2490712b67d draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
| author | bgruening |
|---|---|
| date | Sun, 01 Nov 2015 10:35:04 -0500 |
| parents | 0916781bc971 |
| children | e44dda38e6ae |
| files | osra.tar.bz2 osra.xml repository_dependencies.xml tool_dependencies.xml |
| diffstat | 4 files changed, 17 insertions(+), 13 deletions(-) [+] |
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--- a/osra.xml Sun Apr 20 09:03:07 2014 -0400 +++ b/osra.xml Sun Nov 01 10:35:04 2015 -0500 @@ -6,19 +6,21 @@ <requirement type="package" version="1.3.18">graphicsmagick</requirement> </requirements> <command interpreter='python'> +<![CDATA[ ## 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 + 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 - + $confidence $adaptive $thinning - + > $outfile +]]> </command> <inputs> <param name="infile" type="data" format="png,pdf" label="Image or PDF with molecules"/> @@ -49,9 +51,10 @@ <param name="oformat" value="can"/> <output name="outfile" ftype="sdf" file="2008001635_153_chem.smi"/> </test> - + </tests> <help> +<![CDATA[ .. class:: infomark @@ -70,5 +73,6 @@ Igor V Filippov and Marc C Nicklaus - `Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution`_ .. _`Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution`: http://pubs.acs.org/doi/abs/10.1021/ci800067r +]]> </help> </tool>
--- a/repository_dependencies.xml Sun Apr 20 09:03:07 2014 -0400 +++ b/repository_dependencies.xml Sun Nov 01 10:35:04 2015 -0500 @@ -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="85eca06eefc6" name="molecule_datatypes" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="85eca06eefc6" name="molecule_datatypes" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </repositories>
--- a/tool_dependencies.xml Sun Apr 20 09:03:07 2014 -0400 +++ b/tool_dependencies.xml Sun Nov 01 10:35:04 2015 -0500 @@ -1,10 +1,10 @@ <?xml version="1.0"?> <tool_dependency> <package name="openbabel" version="2.3.2"> - <repository changeset_revision="99a10425de93" name="package_openbabel_2_3" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="e5ef70185d24" name="package_openbabel_2_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="graphicsmagick" version="1.3.18"> - <repository changeset_revision="4ce7b22bf603" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="ef238a8bdc1d" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="osra" version="2.0.0"> <install version="1.0"> @@ -14,20 +14,20 @@ <!-- populate the environment variables from the dependend repos --> <action type="set_environment_for_install"> - <repository changeset_revision="99a10425de93" name="package_openbabel_2_3" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> + <repository changeset_revision="e5ef70185d24" name="package_openbabel_2_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> <package name="openbabel" version="2.3.2" /> </repository> - <repository changeset_revision="4ce7b22bf603" name="package_graphicsmagick_1_3" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> + <repository changeset_revision="ef238a8bdc1d" name="package_graphicsmagick_1_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> <package name="graphicsmagick" version="1.3.18" /> </repository> </action> <!--compiling potrace-1.11 --> - <action type="download_file">http://potrace.sourceforge.net/download/potrace-1.11.tar.gz</action> + <action type="download_file">http://potrace.sourceforge.net/download/1.11/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 + <!-- not yet possible <action type="download_file">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=$INSTALL_DIR/gocr/build && make libs && make all install</action> --> @@ -49,7 +49,7 @@ <!--And finally OSRA 1.4.0--> <!-- Extending the PATH is needed for OSRA --> - <action type="shell_command">export PATH=$PATH:$GRAPHICSMAGICK_ROOT_DIR/bin/ && + <action type="shell_command">export PATH=$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=$INSTALL_DIR/cuneiform/build/include/ --with-cuneiform --with-cuneiform-lib=$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>