# HG changeset patch
# User bgruening
# Date 1446392090 18000
# Node ID 4f0d88f40ea1e6638b81268e08841eeeac0744b2
# Parent  e5e3d723a675dec71b5c4fbc30a18088c4cc195e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit a44c0a13283e873a740eabcad04f021208290dfe-dirty

diff -r e5e3d723a675 -r 4f0d88f40ea1 osra.tar.bz2
Binary file osra.tar.bz2 has changed
diff -r e5e3d723a675 -r 4f0d88f40ea1 osra.xml
--- a/osra.xml	Tue Jul 23 14:53:48 2013 +0200
+++ b/osra.xml	Sun Nov 01 10:34:50 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>
diff -r e5e3d723a675 -r 4f0d88f40ea1 repository_dependencies.xml
--- a/repository_dependencies.xml	Tue Jul 23 14:53:48 2013 +0200
+++ b/repository_dependencies.xml	Sun Nov 01 10:34:50 2015 -0500
@@ -1,4 +1,4 @@
-<?xml version='1.0' encoding='utf-8'?>
+<?xml version="1.0"?>
 <repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format).">
-    <repository changeset_revision="18ff2d6e1dca" name="molecule_datatypes" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
-</repositories>
\ No newline at end of file
+    <repository changeset_revision="8714f927a6ee" name="molecule_datatypes" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+</repositories>
diff -r e5e3d723a675 -r 4f0d88f40ea1 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jul 23 14:53:48 2013 +0200
+++ b/tool_dependencies.xml	Sun Nov 01 10:34:50 2015 -0500
@@ -1,10 +1,10 @@
-<?xml version='1.0' encoding='utf-8'?>
+<?xml version="1.0"?>
 <tool_dependency>
     <package name="openbabel" version="2.3.2">
-        <repository changeset_revision="3a993ff17df5" name="package_openbabel_2_3" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+        <repository changeset_revision="ac9bf7ac1281" name="package_openbabel_2_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <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/" />
+        <repository changeset_revision="bff3f66adff2" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="osra" version="2.0.0">
         <install version="1.0">
@@ -14,43 +14,43 @@
 
                 <!-- populate the environment variables from the dependend repos -->
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="3a993ff17df5" name="package_openbabel_2_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/">
+                    <repository changeset_revision="ac9bf7ac1281" name="package_openbabel_2_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="openbabel" version="2.3.2" />
                     </repository>
-                    <repository changeset_revision="34f511310435" name="package_graphicsmagick_1_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/">
+                    <repository changeset_revision="bff3f66adff2" name="package_graphicsmagick_1_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="graphicsmagick" version="1.3.18" />
                     </repository>
                 </action>
 
                 <!--compiling potrace-1.11 -->
-                <action type="shell_command">wget 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 &amp;&amp; cd potrace-1.11 &amp;&amp; ./configure --with-libpotrace --prefix=$INSTALL_DIR/potrace/build &amp;&amp; make &amp;&amp; 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>
+                <!-- 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 &amp;&amp; cd gocr-0.50 &amp;&amp; ./configure -|-prefix=$INSTALL_DIR/gocr/build &amp;&amp; make libs &amp;&amp; make all install</action>
                 -->
-                <action type="shell_command">wget http://downloads.sourceforge.net/project/osra/gocr-patched/gocr-0.50pre-patched.tgz</action>
+                <action type="download_file">http://downloads.sourceforge.net/project/osra/gocr-patched/gocr-0.50pre-patched.tgz</action>
                 <action type="shell_command">tar xfvz gocr-0.50pre-patched.tgz &amp;&amp; cd gocr-0.50pre-patched &amp;&amp; ./configure --prefix=$INSTALL_DIR/gocr/build &amp;&amp; make libs &amp;&amp; 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="download_file">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 &amp;&amp; cd tclap-1.2.1 &amp;&amp; ./configure --prefix=$INSTALL_DIR/tclap/build &amp;&amp; make &amp;&amp; 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="download_file">http://mirror.checkdomain.de/gnu/ocrad/ocrad-0.21.tar.gz</action>
                 <action type="shell_command">tar xfvz ocrad-0.21.tar.gz &amp;&amp; cd ocrad-0.21 &amp;&amp; ./configure --prefix=$INSTALL_DIR/ocrad/build &amp;&amp; make &amp;&amp; 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="download_file">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 &amp;&amp; cd cuneiform-linux-1.1.0 &amp;&amp; mkdir build &amp;&amp; cd build &amp;&amp; cmake .. -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/cuneiform/build/ &amp;&amp; make &amp;&amp; make install</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/ &amp;&amp; 
-                    ./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">export PATH=$PATH:$GRAPHICSMAGICK_ROOT_DIR/bin/ &amp;&amp;
+                    ./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>
 
@@ -71,4 +71,4 @@
         </install>
         <readme>We still have a handfull of requirements</readme>
     </package>
-</tool_dependency>
\ No newline at end of file
+</tool_dependency>
diff -r e5e3d723a675 -r 4f0d88f40ea1 tool_dependencies_1_4.xml
--- a/tool_dependencies_1_4.xml	Tue Jul 23 14:53:48 2013 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,69 +0,0 @@
-<tool_dependency>
-    <package name="openbabel" version="2.3.2">
-        <repository name="package_openbabel_2_3" owner="bgruening" prior_installation_required="True" />
-    </package>
-    <package name="graphicsmagick" version="1.3.18">
-        <repository name="package_graphicsmagick_1_3" owner="bgruening" prior_installation_required="True" />
-    </package>
-    <package name="osra" version="1.4.0">
-        <install version="1.0">
-            <actions>
-                <!-- first action is always downloading -->
-                <action type="download_by_url">http://downloads.sourceforge.net/project/osra/osra/1.4.0/osra-1.4.0.tgz</action>
-
-                <!-- populate the environment variables from the dependend repos -->
-                <action type="set_environment_for_install">
-                    <repository name="package_openbabel_2_3" owner="bgruening">
-                        <package name="openbabel" version="2.3.2" />
-                    </repository>
-                    <repository name="package_graphicsmagick_1_3" owner="bgruening">
-                        <package name="graphicsmagick" version="1.3.18" />
-                    </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 &amp;&amp; cd potrace-1.11 &amp;&amp; ./configure --with-libpotrace --prefix=$INSTALL_DIR/potrace/build &amp;&amp; make &amp;&amp; make install</action>
-
-                <!--compiling gocr 0.50patched -->
-                <action type="shell_command">wget http://downloads.sourceforge.net/project/osra/gocr-patched/gocr-0.50pre-patched.tgz</action>
-                <action type="shell_command">tar xfvz gocr-0.50pre-patched.tgz &amp;&amp; cd gocr-0.50pre-patched &amp;&amp; ./configure --prefix=$INSTALL_DIR/gocr/build &amp;&amp; make libs &amp;&amp; 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 &amp;&amp; cd tclap-1.2.1 &amp;&amp; ./configure --prefix=$INSTALL_DIR/tclap/build &amp;&amp; make &amp;&amp; make install</action>
-
-                <!--compiling ocrad 0.21 -->
-                <action type="shell_command">wget http://mirror.checkdomain.de/gnu/ocrad/ocrad-0.21.tar.gz</action>
-                <action type="shell_command">tar xfvz ocrad-0.21.tar.gz &amp;&amp; cd ocrad-0.21 &amp;&amp; ./configure --prefix=$INSTALL_DIR/ocrad/build &amp;&amp; make &amp;&amp; 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 &amp;&amp; cd cuneiform-linux-1.1.0 &amp;&amp; mkdir build &amp;&amp; cd build &amp;&amp; cmake .. -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/cuneiform/build/ &amp;&amp; make &amp;&amp; make install</action>
-
-                <!--And finally OSRA 1.4.0-->
-                <action type="shell_command">wget http://share.gruenings.eu/osra-1.4.0-configure.patch</action>
-                <action type="shell_command">patch configure &lt; osra-1.4.0-configure.patch</action>
-                <!-- Extending the PATH is needed for OSRA -->
-                <action type="shell_command">export PATH=$PATH:$GRAPHICSMAGICK_ROOT_DIR/bin/ &amp;&amp; ./configure --with-tclap-include=$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 $INSTALL_DIR/cuneiform/ -r</action>
-
-                <action type="set_environment">
-                    <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$GRAPHICSMAGICK_ROOT_DIR/lib/</environment_variable>
-                    <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/potrace/build/lib/</environment_variable>
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                    <!-- OSRA_DATA_FILES is only used by the galaxy wrapper and is not part of OSRA -->
-                    <environment_variable name="OSRA_DATA_FILES" action="set_to">$INSTALL_DIR/share</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>We still have a handfull of requirements</readme>
-    </package>
-</tool_dependency>