diff osra.xml @ 2:d2490712b67d draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit a44c0a13283e873a740eabcad04f021208290dfe-dirty

--- 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>