# HG changeset patch
# User bgruening
# Date 1446392104 18000
# Node ID d2490712b67d415daa47fb004c0de46689fc9ec4
# Parent  0916781bc9713236e6e3c5a56cdaad05cf44c77d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit a44c0a13283e873a740eabcad04f021208290dfe-dirty

diff -r 0916781bc971 -r d2490712b67d osra.tar.bz2
Binary file osra.tar.bz2 has changed
diff -r 0916781bc971 -r d2490712b67d osra.xml
--- 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>
diff -r 0916781bc971 -r d2490712b67d repository_dependencies.xml
--- 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>
diff -r 0916781bc971 -r d2490712b67d tool_dependencies.xml
--- 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 &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 
+                <!-- 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>
                 -->
@@ -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/ &amp;&amp; 
+                <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>