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changeset 2:125da3a296ca draft default tip

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Uploaded
author bgruening
date Wed, 15 Jul 2015 12:13:08 -0400
parents b52872a1755a
children
files convert/ob_convert.xml filter/multi_obgrep.xml filter/ob_filter.xml filter/ob_grep.xml filter/ob_remDuplicates.xml filter/ob_remIons.xml filter/ob_remSmall.xml modify/change_title_to_metadata_value.xml modify/ob_addh.xml modify/ob_genProp.xml modify/remove_protonation_state.xml repository_dependencies.xml search/ob_spectrophore_search.xml subsearch/subsearch.xml tool_dependencies.xml visualisation/ob_depiction_svg.xml
diffstat 16 files changed, 226 insertions(+), 170 deletions(-) [+]
line wrap: on
line diff
--- 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>
--- a/filter/multi_obgrep.xml	Wed Aug 21 03:06:02 2013 -0400
+++ b/filter/multi_obgrep.xml	Wed Jul 15 12:13:08 2015 -0400
@@ -4,6 +4,7 @@
         <requirement type="package" version="2.3.2">openbabel</requirement>
     </requirements>
     <command interpreter="python">
+<![CDATA[
 
     multi_obgrep.py
         -i $infile
@@ -15,8 +16,9 @@
         $only_name
         $full_match
         $number_of_matches
-        --processors 10
+        --processors "\${GALAXY_SLOTS:-12}"
 
+]]>
     </command>
     <inputs>
         <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Compound File" help="Specify a compound file in SDF Format"/>
@@ -35,6 +37,7 @@
         </test>
     </tests>
     <help>
+<![CDATA[
 
 .. class:: infomark
 
@@ -80,5 +83,6 @@
 
 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page
 
+]]>
     </help>
 </tool>
--- a/filter/ob_filter.xml	Wed Aug 21 03:06:02 2013 -0400
+++ b/filter/ob_filter.xml	Wed Jul 15 12:13:08 2015 -0400
@@ -6,6 +6,7 @@
     <requirement type="package" version="0.1">cheminfolib</requirement>
   </requirements>
   <command interpreter="python">
+<![CDATA[
     ob_filter.py
       -i "${infile}"
       -o "${outfile}"
@@ -40,6 +41,7 @@
           #end for
         #end if
       }'
+]]>
   </command>
   <inputs>
     <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi" label="Select input file previously created with the 'Compute physico-chemical properties' tool"/>
@@ -136,13 +138,14 @@
     -->
   </tests>
   <help>
+<![CDATA[
 
 
 .. class:: infomark
 
 **What this tool does**
 
-Filters a library of compounds based on user-defined physico-chemical parameters or predefined options (e.g. Ro5, lead-like properties, etc.). Multiple parameters can be selected for more specific queries. 
+Filters a library of compounds based on user-defined physico-chemical parameters or predefined options (e.g. Ro5, lead-like properties, etc.). Multiple parameters can be selected for more specific queries.
 
 -----
 
@@ -151,9 +154,9 @@
 **Hint**
 
 | If your input file is in SDF format you can use the *Compute physico-chemical properties* tool to precalulate the properties and use the filter on that precomputed dataset. It should be faster and can be reused but it's bigger than a SMILES file.
-| 
+|
 | For exact matches please use the target value for both minimum and maximum parameters (e.g. a selection of exactly 4 rotatable bonds can be performed by selecting 4 as minimum and maximum value).
-| 
+|
 | Selecting the same property multiple times with different parameters will result in querying the largest overlapping subset of values for the parameter (e.g. a selection of between 0 and 3 rotatable bonds plus a selection between 2 and 4 will result in a query for compounds between 2 and 3 rotatable bonds).
 
 -----
@@ -163,38 +166,38 @@
 **Definition of the pre-defined filtering rules**
 
   **# Lipinski's Rule of Five:**
-    =&lt; 5 Hydrogen-bond donor groups
+    =< 5 Hydrogen-bond donor groups
 
-    =&lt; 10 Hydrogen-bond acceptor groups
+    =< 10 Hydrogen-bond acceptor groups
 
-    =&lt; 500 Molecular weight
+    =< 500 Molecular weight
 
-    =&lt; 5 octanol/water partition coefficient (log P)
+    =< 5 octanol/water partition coefficient (log P)
 
   **# Lead Like properties** (Teague, Davis, Leeson, Oprea, Angew Chem Int Ed Engl. 1999 Dec 16;38(24):3743-3748):
-    =&lt; 7 rotatable bonds
+    =< 7 rotatable bonds
 
-    =&lt; 350 Molecular weight
+    =< 350 Molecular weight
 
-    =&lt; 3.5 octanol/water partition coefficient (log P)
+    =< 3.5 octanol/water partition coefficient (log P)
 
   **# Drug Like properties** (Lipinski, J Pharmacol Toxicol Methods. 2000 Jul-Aug;44(1):235-49):
-    =&lt; 10 Hydrogen-bond acceptor groups
+    =< 10 Hydrogen-bond acceptor groups
 
-    =&lt; 8 rotatable bonds
+    =< 8 rotatable bonds
 
-    150 =&lt; Molecular weight =&lt; 500
+    150 =< Molecular weight =< 500
 
-    =&lt; 150 Polar Surface Area
+    =< 150 Polar Surface Area
 
-    =&lt; 5 octanol/water partition coefficient (log P)
+    =< 5 octanol/water partition coefficient (log P)
 
   **# Fragment Like properties** (Carr RA, Congreve M, Murray CW, Rees DC, Drug Discov Today. 2005 Jul 15;10(14):987):
-    =&lt; 5 rotatable bonds
+    =< 5 rotatable bonds
 
-    =&lt; 250 Molecular weight
+    =< 250 Molecular weight
 
-    =&lt; 2.5 octanol/water partition coefficient (log P)
+    =< 2.5 octanol/water partition coefficient (log P)
 
 -----
 
@@ -212,10 +215,10 @@
 
 .. class:: infomark
 
-**Output** 
+**Output**
 
 | SDF formatted coordinates of the molecules, with selected properties stored as meta-data for each compound.
-| 
+|
 | SMILES, InChI or mol2 formatted files containing the 1D strings or 3D coordinates of each compound.
 
 -----
@@ -236,5 +239,6 @@
 
 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page
 
+]]>
   </help>
 </tool>
--- a/filter/ob_grep.xml	Wed Aug 21 03:06:02 2013 -0400
+++ b/filter/ob_grep.xml	Wed Jul 15 12:13:08 2015 -0400
@@ -5,6 +5,7 @@
         <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
         obgrep
@@ -20,7 +21,8 @@
         -i ${infile.ext}
         "${smarts_pattern}"
         "${infile}"
-        > "${outfile}" 2>&#38;1
+        > "${outfile}" 2>&1
+]]>
     </command>
     <inputs>
         <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Compound File" help="Specify a compound file in SDF Format."/>
@@ -48,6 +50,7 @@
     </test>
     </tests>
     <help>
+<![CDATA[
 
 .. class:: infomark
 
@@ -94,5 +97,6 @@
 
 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page
 
+]]>
     </help>
 </tool>
--- a/filter/ob_remDuplicates.xml	Wed Aug 21 03:06:02 2013 -0400
+++ b/filter/ob_remDuplicates.xml	Wed Jul 15 12:13:08 2015 -0400
@@ -5,6 +5,7 @@
         <requirement type="package" version="2.3.2">openbabel</requirement>
     </requirements>
   <command>
+<![CDATA[
     obabel
       -i"${infile.ext}"
        "${infile}"
@@ -12,7 +13,8 @@
       --unique "${descriptor}"
       -O "${outfile}"
       -e
-      2>&#38;1
+      2>&1
+]]>
   </command>
   <inputs>
     <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Molecular input file"/>
@@ -33,6 +35,7 @@
     </test>
   </tests>
   <help>
+<![CDATA[
 
 .. class:: infomark
 
@@ -64,7 +67,7 @@
 
 .. class:: infomark
 
-**Output** 
+**Output**
 
 Same as input format.
 
@@ -82,5 +85,6 @@
 
 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page
 
+]]>
   </help>
 </tool>
--- a/filter/ob_remIons.xml	Wed Aug 21 03:06:02 2013 -0400
+++ b/filter/ob_remIons.xml	Wed Jul 15 12:13:08 2015 -0400
@@ -5,10 +5,12 @@
         <requirement type="package" version="2.3.2">openbabel</requirement>
     </requirements>
     <command interpreter="python">
+<![CDATA[
     ob_remIons.py
       -i "${infile}"
       -iformat "${infile.ext}"
       -o "${outfile}"
+]]>
     </command>
     <inputs>
         <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Select input file with multiple molecules"/>
@@ -23,6 +25,7 @@
         </test>
     </tests>
     <help>
+<![CDATA[
 
 .. class:: infomark
 
@@ -37,7 +40,7 @@
 **Hint**
 
 | Only the **largest fragment** on every molecule is extracted.
-| 
+|
 | Only molecules with more than 5 heavy atoms are parsed.
 
 -----
@@ -58,5 +61,6 @@
 
 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page
 
+]]>
     </help>
 </tool>
--- a/filter/ob_remSmall.xml	Wed Aug 21 03:06:02 2013 -0400
+++ b/filter/ob_remSmall.xml	Wed Jul 15 12:13:08 2015 -0400
@@ -5,6 +5,7 @@
         <requirement type="package" version="2.3.2">openbabel</requirement>
     </requirements>
     <command>
+<![CDATA[
     obabel
       -i"${infile.ext}"
       "${infile}"
@@ -12,7 +13,8 @@
       -O "${outfile}"
       --filter "atoms > $cutoff"
       -e
-      2>&#38;1
+      2>&1
+]]>
     </command>
     <inputs>
         <param name="infile" format="sdf,mol,mol2,cml,inchi,smi" type="data" label="Molecular input file" />
@@ -29,6 +31,7 @@
         </test>
     </tests>
     <help>
+<![CDATA[
 
 .. class:: infomark
 
@@ -66,5 +69,6 @@
 
 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page
 
+]]>
     </help>
 </tool>
--- a/modify/change_title_to_metadata_value.xml	Wed Aug 21 03:06:02 2013 -0400
+++ b/modify/change_title_to_metadata_value.xml	Wed Jul 15 12:13:08 2015 -0400
@@ -5,12 +5,14 @@
         <requirement type="package" version="2.3.2">openbabel</requirement>
     </requirements>
     <command interpreter="python">
+<![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
         change_title_to_metadata_value.py
         --infile "${infile}"
         --key "${key}"
         --outfile "${outfile}"
+]]>
     </command>
     <inputs>
         <param name="infile" type="data" format="sdf,mol2" label="Compound File" help="Specify a compound file in SD- or MOL2-format."/>
@@ -25,6 +27,7 @@
         <data name="output" type="sdf" file="change_title_on_CID_3033.sdf"/>
     </tests>
     <help>
+<![CDATA[
 
 .. class:: infomark
 
@@ -60,5 +63,6 @@
 
 .. _Open Babel: http://openbabel.org/wiki/Main_Page
 
+]]>
     </help>
 </tool>
--- a/modify/ob_addh.xml	Wed Aug 21 03:06:02 2013 -0400
+++ b/modify/ob_addh.xml	Wed Jul 15 12:13:08 2015 -0400
@@ -5,12 +5,14 @@
         <requirement type="package" version="2.3.2">openbabel</requirement>
     </requirements>
     <command interpreter="python">
+<![CDATA[
     ob_addh.py
       -i "${infile}"
       --iformat "${infile.ext}"
       -o "${outfile}"
       $polar
       --pH "${pH_value}"
+]]>
     </command>
     <inputs>
         <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi" label="Select input file"/>
@@ -29,6 +31,7 @@
         </test>
     </tests>
     <help>
+<![CDATA[
 
 .. class:: infomark
 
@@ -55,7 +58,7 @@
 
 .. class:: warningmark
 
-**Hint** 
+**Hint**
 
 To avoid possible crashes, only molecules with more than five heavy atoms are parsed.
 
@@ -63,7 +66,7 @@
 
 .. class:: infomark
 
-**Output** 
+**Output**
 
 Same output format as the input format.
 
@@ -81,5 +84,6 @@
 
 .. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://www.biomedcentral.com/content/pdf/1752-153X-2-5.pdf
 
+]]>
     </help>
 </tool>
--- a/modify/ob_genProp.xml	Wed Aug 21 03:06:02 2013 -0400
+++ b/modify/ob_genProp.xml	Wed Jul 15 12:13:08 2015 -0400
@@ -6,6 +6,7 @@
         <requirement type="package" version="0.1">cheminfolib</requirement>
     </requirements>
     <command interpreter="python">
+<![CDATA[
     ob_genProp.py
       -i "${infile}"
       --iformat "${infile.ext}"
@@ -14,6 +15,7 @@
         --header $output_opts.header
       #end if
       -o "${outfile}"
+]]>
   </command>
   <inputs>
     <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Select input file with multiple molecules."/>
@@ -51,6 +53,7 @@
     </test>
   </tests>
   <help>
+<![CDATA[
 
 .. class:: infomark
 
@@ -131,5 +134,6 @@
 .. _Silicos: http://openbabel.org/docs/dev/Fingerprints/spectrophore.html
 
 
+]]>
   </help>
 </tool>
--- a/modify/remove_protonation_state.xml	Wed Aug 21 03:06:02 2013 -0400
+++ b/modify/remove_protonation_state.xml	Wed Jul 15 12:13:08 2015 -0400
@@ -5,11 +5,13 @@
         <requirement type="package" version="2.3.2">openbabel</requirement>
     </requirements>
     <command interpreter='python'>
+<![CDATA[
     remove_protonation_state.py
         -i $infile
         -o $outfile
         --iformat "${infile.ext}"
-        2>&#38;1
+        2>&1
+]]>
     </command>
     <inputs>
         <param name="infile" type="data" format="sdf,smi,mol,inchi" label="Molecule file" help="Dataset missing? See TIP below"/>
@@ -22,6 +24,7 @@
         </test>
     </tests>
     <help>
+<![CDATA[
 
 .. class:: infomark
 
@@ -39,5 +42,6 @@
 
 .. _Open Babel: http://openbabel.org/wiki/Main_Page
 
+]]>
     </help>
 </tool>
--- a/repository_dependencies.xml	Wed Aug 21 03:06:02 2013 -0400
+++ b/repository_dependencies.xml	Wed Jul 15 12:13:08 2015 -0400
@@ -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/search/ob_spectrophore_search.xml	Wed Aug 21 03:06:02 2013 -0400
+++ b/search/ob_spectrophore_search.xml	Wed Jul 15 12:13:08 2015 -0400
@@ -5,11 +5,13 @@
     <requirement type="package" version="1.7.1">numpy</requirement>
   </requirements>
   <command interpreter="python">
+<![CDATA[
     ob_spectrophore_search.py
       --target $target
       --library $library
       --output $outfile
       --column $column
+]]>
   </command>
   <inputs>
     <param name="target" type="data" format="sdf" label="Target molecule in SDF format (it must contain its Spectrophores(TM) stored as meta-data)"/>
@@ -28,6 +30,7 @@
     </test>
   </tests>
   <help>
+<![CDATA[
 
 .. class:: infomark
 
@@ -59,7 +62,7 @@
 
 .. class:: infomark
 
-**Input** 
+**Input**
 
 The target molecule must be a SD formatted file with the |Spectrophores (TM)| descriptors stored as metadata. Such files can be generated using the *Compute physico-chemical properties* tool.
 
@@ -84,5 +87,6 @@
 .. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://www.biomedcentral.com/content/pdf/1752-153X-2-5.pdf
 .. _Silicos: http://openbabel.org/docs/dev/Fingerprints/spectrophore.html
 
+]]>
   </help>
 </tool>
--- a/subsearch/subsearch.xml	Wed Aug 21 03:06:02 2013 -0400
+++ b/subsearch/subsearch.xml	Wed Jul 15 12:13:08 2015 -0400
@@ -4,16 +4,18 @@
         <requirement type="package" version="2.3.2">openbabel</requirement>
     </requirements>
     <command interpreter="python">
+<![CDATA[
 
     subsearch.py
         -i $query
         --iformat "${query.ext}"
-        --fastsearch-index "${os.path.join($fastsearch.extra_files_path,'molecule.fs')}"
+        --fastsearch-index "${os.path.join($fastsearch.files_path,'molecule.fs')}"
         -o "${outfile}"
         --oformat $oformat
         --max-candidates $max_candidates
-        --processors 10
+        --processors "\${GALAXY_SLOTS:-12}"
 
+]]>
     </command>
     <inputs>
         <param name="query" type='data' format="tabular,smi,sdf,inchi,text" label="query"/>
@@ -42,6 +44,7 @@
         </test>
     </tests>
     <help>
+<![CDATA[
 
 .. class:: infomark
 
@@ -69,5 +72,6 @@
 
 .. _Open Babel: http://openbabel.org/wiki/Main_Page
 
+]]>
     </help>
 </tool>
--- a/tool_dependencies.xml	Wed Aug 21 03:06:02 2013 -0400
+++ b/tool_dependencies.xml	Wed Jul 15 12:13:08 2015 -0400
@@ -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" 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>
     <package name="numpy" version="1.7.1">
-        <repository changeset_revision="74c21f9bdc39" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="8b3a5c7061d8" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="cheminfolib" version="0.1">
         <install version="1.0">
--- a/visualisation/ob_depiction_svg.xml	Wed Aug 21 03:06:02 2013 -0400
+++ b/visualisation/ob_depiction_svg.xml	Wed Jul 15 12:13:08 2015 -0400
@@ -1,127 +1,131 @@
-<tool id="ctb_ob_svg_depiction" name="Visualisation">
-    <description>of compounds</description>
-    <requirements>
-        <requirement type="package" version="2.3.2">openbabel</requirement>
-    </requirements>
-    <command>
-    obabel -i${infile.ext} $infile
-        $embed_molecule_as_cml
-        $draw_all_carbon_atoms
-        -xC 
-        -O 
-        $outfile -o$oformat
-        #if str($sort) != "none":
-            --sort $sort
-        #end if
-        #if str($display_name) != "None" and len(str($display_name)) > 0 and str($display_name) != 'title':
-            --append "$display_name"
-            --title ""
-        #end if
-        $thick_lines
-    2>&#38;1
-    </command>
-    <inputs>
-        <param name="infile" type="data" format="mol,sdf,smi,inchi" label="Input format"/>
-        <param name="embed_molecule_as_cml" type="boolean" truevalue="-e" falsevalue="" label="Embed molecule as CML"/>
-        <param name="draw_all_carbon_atoms" type="boolean" truevalue="-a" falsevalue="" label="draw all carbon atoms"/>
-        <param name="thick_lines" type="boolean" truevalue="-xt" falsevalue="" label="use thicker lines"/>
-
-        <param name='display_name' type='select' format='text' label="The property which is displayed under the molecule">
-            <option value='title'>Molecule's title</option>
-            <option value='MW'>Molecular Weight</option>
-            <option value='abonds'>Number of aromatic bonds</option>
-            <option value='atoms'>Number of atoms</option>
-            <option value='bonds'>Number of bonds</option>
-            <option value='cansmi'>Canonical SMILES</option>
-            <option value='cansmiNS'>Canonical SMILES without isotopes or stereo</option>
-            <option value='dbonds'>Number of double bonds</option>
-            <option value='formula'>Chemical formula</option>
-            <option value='HBA1'>Number of Hydrogen Bond Acceptors 1 (JoelLib)</option>
-            <option value='HBA2'>Number of Hydrogen Bond Acceptors 2 (JoelLib)</option>
-            <option value='HBD'>Number of Hydrogen Bond Donors (JoelLib)</option>
-            <option value='InChI'>IUPAC InChI identifier</option>
-            <option value='L5'>Lipinski Rule of Five</option>
-            <option value='logP'>octanol/water partition coefficient</option>
-            <option value='MR'>molar refractivity</option>
-            <option value='nF'>Number of Fluorine Atoms</option>
-            <option value='s'>SMARTS filter</option>
-            <option value='sbonds'>Number of single bonds</option>
-            <option value='smarts'>SMARTS filter</option>
-            <option value='tbonds'>Number of triple bonds</option>
-            <option value='TPSA'>topological polar surface area</option>
-        </param>
-
-        <param name='sort' type='select' format='text' label="Sorting the displayed molecules by">
-            <option value='none'>No sorting</option>
-            <option value='MW'>Molecular Weight</option>
-            <option value='abonds'>Number of aromatic bonds</option>
-            <option value='atoms'>Number of atoms</option>
-            <option value='bonds'>Number of bonds</option>
-            <option value='dbonds'>Number of double bonds</option>
-            <option value='HBA1'>Number of Hydrogen Bond Acceptors 1 (JoelLib)</option>
-            <option value='HBA2'>Number of Hydrogen Bond Acceptors 2 (JoelLib)</option>
-            <option value='HBD'>Number of Hydrogen Bond Donors (JoelLib)</option>
-            <option value='L5'>Lipinski Rule of Five</option>
-            <option value='logP'>octanol/water partition coefficient</option>
-            <option value='MR'>molar refractivity</option>
-            <option value='nF'>Number of Fluorine Atoms</option>
-            <option value='sbonds'>Number of single bonds</option>
-            <option value='tbonds'>Number of triple bonds</option>
-            <option value='TPSA'>topological polar surface area</option>
-        </param>
-
-        <param name='oformat' type='select' format='text' label="Format of the resulting picture">
-            <option value='svg'>SVG</option>
-            <option value='png'>PNG</option>
-        </param>
-
-    </inputs>
-    <outputs>
-        <data name="outfile" type="data" format="png" label="${tool.name} on ${on_string}">
-            <change_format>
-                <when input="oformat" value="svg" format="svg"/>
-            </change_format>
-        </data>
-    </outputs>
-    <tests>
-        <test>
-            <param name="infile" ftype="smi" value="8_mol.smi" />
-            <param name="embed_molecule_as_cml" value="" />
-            <param name="draw_all_carbon_atoms" value="-a" />
-            <param name="thick_lines" value="-xt" />
-            <param name='display_name' value="title" />
-            <param name='sort' value='none' />
-            <output name="outfile" ftype="svg" file="ob_depiction_svg_on_8_mol.svg" />
-        </test>
-    </tests>
-    <help>
-
-.. class:: infomark
-
-**What this tool does**
-
-Creates an .svg or .png image of a small set of molecules (few hundreds). Based on Open Babel PNG_/SVG_ 2D depiction.
-
-.. _PNG: http://openbabel.org/docs/dev/FileFormats/PNG_2D_depiction.html
-.. _SVG: http://openbabel.org/docs/dev/FileFormats/SVG_2D_depiction.html
-
------
-
-.. class:: warningmark
-
-**Hint**
-
-Use only libraries with at most a few hundred molecules.
-
------
-
-.. class:: infomark
-
-**Cite**
-
-`Open Babel`_
-
-.. _Open Babel: http://openbabel.org/wiki/Main_Page
-
-  </help>
-</tool>
+<tool id="ctb_ob_svg_depiction" name="Visualisation">
+    <description>of compounds</description>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+    obabel -i${infile.ext} $infile
+        $embed_molecule_as_cml
+        $draw_all_carbon_atoms
+        -xC
+        -O
+        $outfile -o$oformat
+        #if str($sort) != "none":
+            --sort $sort
+        #end if
+        #if str($display_name) != "None" and len(str($display_name)) > 0 and str($display_name) != 'title':
+            --append "$display_name"
+            --title ""
+        #end if
+        $thick_lines
+    2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="mol,sdf,smi,inchi" label="Input format"/>
+        <param name="embed_molecule_as_cml" type="boolean" truevalue="-e" falsevalue="" label="Embed molecule as CML"/>
+        <param name="draw_all_carbon_atoms" type="boolean" truevalue="-a" falsevalue="" label="draw all carbon atoms"/>
+        <param name="thick_lines" type="boolean" truevalue="-xt" falsevalue="" label="use thicker lines"/>
+
+        <param name='display_name' type='select' format='text' label="The property which is displayed under the molecule">
+            <option value='title'>Molecule's title</option>
+            <option value='MW'>Molecular Weight</option>
+            <option value='abonds'>Number of aromatic bonds</option>
+            <option value='atoms'>Number of atoms</option>
+            <option value='bonds'>Number of bonds</option>
+            <option value='cansmi'>Canonical SMILES</option>
+            <option value='cansmiNS'>Canonical SMILES without isotopes or stereo</option>
+            <option value='dbonds'>Number of double bonds</option>
+            <option value='formula'>Chemical formula</option>
+            <option value='HBA1'>Number of Hydrogen Bond Acceptors 1 (JoelLib)</option>
+            <option value='HBA2'>Number of Hydrogen Bond Acceptors 2 (JoelLib)</option>
+            <option value='HBD'>Number of Hydrogen Bond Donors (JoelLib)</option>
+            <option value='InChI'>IUPAC InChI identifier</option>
+            <option value='L5'>Lipinski Rule of Five</option>
+            <option value='logP'>octanol/water partition coefficient</option>
+            <option value='MR'>molar refractivity</option>
+            <option value='nF'>Number of Fluorine Atoms</option>
+            <option value='s'>SMARTS filter</option>
+            <option value='sbonds'>Number of single bonds</option>
+            <option value='smarts'>SMARTS filter</option>
+            <option value='tbonds'>Number of triple bonds</option>
+            <option value='TPSA'>topological polar surface area</option>
+        </param>
+
+        <param name='sort' type='select' format='text' label="Sorting the displayed molecules by">
+            <option value='none'>No sorting</option>
+            <option value='MW'>Molecular Weight</option>
+            <option value='abonds'>Number of aromatic bonds</option>
+            <option value='atoms'>Number of atoms</option>
+            <option value='bonds'>Number of bonds</option>
+            <option value='dbonds'>Number of double bonds</option>
+            <option value='HBA1'>Number of Hydrogen Bond Acceptors 1 (JoelLib)</option>
+            <option value='HBA2'>Number of Hydrogen Bond Acceptors 2 (JoelLib)</option>
+            <option value='HBD'>Number of Hydrogen Bond Donors (JoelLib)</option>
+            <option value='L5'>Lipinski Rule of Five</option>
+            <option value='logP'>octanol/water partition coefficient</option>
+            <option value='MR'>molar refractivity</option>
+            <option value='nF'>Number of Fluorine Atoms</option>
+            <option value='sbonds'>Number of single bonds</option>
+            <option value='tbonds'>Number of triple bonds</option>
+            <option value='TPSA'>topological polar surface area</option>
+        </param>
+
+        <param name='oformat' type='select' format='text' label="Format of the resulting picture">
+            <option value='svg'>SVG</option>
+            <option value='png'>PNG</option>
+        </param>
+
+    </inputs>
+    <outputs>
+        <data name="outfile" type="data" format="png" label="${tool.name} on ${on_string}">
+            <change_format>
+                <when input="oformat" value="svg" format="svg"/>
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" ftype="smi" value="8_mol.smi" />
+            <param name="embed_molecule_as_cml" value="" />
+            <param name="draw_all_carbon_atoms" value="-a" />
+            <param name="thick_lines" value="-xt" />
+            <param name='display_name' value="title" />
+            <param name='sort' value='none' />
+            <output name="outfile" ftype="svg" file="ob_depiction_svg_on_8_mol.svg" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+.. class:: infomark
+
+**What this tool does**
+
+Creates an .svg or .png image of a small set of molecules (few hundreds). Based on Open Babel PNG_/SVG_ 2D depiction.
+
+.. _PNG: http://openbabel.org/docs/dev/FileFormats/PNG_2D_depiction.html
+.. _SVG: http://openbabel.org/docs/dev/FileFormats/SVG_2D_depiction.html
+
+-----
+
+.. class:: warningmark
+
+**Hint**
+
+Use only libraries with at most a few hundred molecules.
+
+-----
+
+.. class:: infomark
+
+**Cite**
+
+`Open Babel`_
+
+.. _Open Babel: http://openbabel.org/wiki/Main_Page
+
+]]>
+  </help>
+</tool>