diff convert/ob_convert.xml @ 2:125da3a296ca draft default tip

Uploaded

--- a/convert/ob_convert.xml	Wed Aug 21 03:06:02 2013 -0400
+++ b/convert/ob_convert.xml	Wed Jul 15 12:13:08 2015 -0400
@@ -8,6 +8,7 @@
         <requirement type="package" version="2.3.2">openbabel</requirement>
     </requirements>
     <command>
+<![CDATA[
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
 
@@ -16,17 +17,17 @@
     #if $format == "fs":
         ## For the fastsearch index we need to copy the original molecule files to the composite datatype of obfs.
         ## Because openbabel likes file extensions, we give the molecule file a proper file extension.
-        mkdir $outfile.extra_files_path;
-        cp "${infile}" ${os.path.join($outfile.extra_files_path, 'molecule.%s' % $infile.ext )};
+        mkdir $outfile.files_path;
+        cp "${infile}" ${os.path.join($outfile.files_path, 'molecule.%s' % $infile.ext )};
     #end if
 
 obabel -i "${infile.ext}"
 
     #if $format == "fs":
         ## the fs filetype need his own symlink path, all others can take the original ones
-        ${os.path.join($outfile.extra_files_path, 'molecule.%s' % $infile.ext )}
+        ${os.path.join($outfile.files_path, 'molecule.%s' % $infile.ext )}
         -o "$format" -e
-        -O ${os.path.join($outfile.extra_files_path,'molecule.fs')}
+        -O ${os.path.join($outfile.files_path,'molecule.fs')}
         #if int($oformat.fs_fold) > 0:
             -xN$oformat.fs_fold
         #end if
@@ -125,7 +126,8 @@
         -p $ph
     #end if
 
-    2>&#38;1
+    2>&1
+]]>
     </command>
     <inputs>
         <param name="infile" type="data" format="sdf,mol2,cml,inchi,smi" label="Select input file with molecules"/>
@@ -145,7 +147,7 @@
                 <option value="cdxml">ChemDraw CDXML format</option>
                 <option value="cht">Chemtool format</option>
                 <option value="cif">Crystallographic Information File</option>
-                <option value="cml">Chemical Markup Language</option>
+                <option value="cml">Chemical Markup Language (CML)</option>
                 <option value="cmlr">CML Reaction format</option>
                 <option value="com">Gaussian 98/03 Cartesian Input</option>
                 <option value="copy">Copies raw text</option>
@@ -424,13 +426,14 @@
         </data>
     </outputs>
     <help>
+<![CDATA[
 
 .. class:: infomark
 
 **What this tool does**
 
-The compound converter joins several `Open Babel`_ command prompt converters in an easy to use tool. It converts various chemistry and moleculare modeling data files. 
-The output format can be specified as well as several parameters. Some parameters are available for all tools (e.g. protonation state and pH) 
+The compound converter joins several `Open Babel`_ command prompt converters in an easy to use tool. It converts various chemistry and moleculare modeling data files.
+The output format can be specified as well as several parameters. Some parameters are available for all tools (e.g. protonation state and pH)
 others are specific for a given output format (e.g. exclude isotopes for conversion to canSMI).
 
 -----
@@ -456,5 +459,6 @@
 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page
 
 
+]]>
   </help>
 </tool>