Mercurial > repos > bgruening > openbabel

changeset 1:e8dce9596b4c

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Uploaded
author bgruening
date Wed, 27 Mar 2013 15:25:33 -0400
parents 6493d130f018
children efe00424f82b
files modify/ob_genProp.xml modify/remove_protonation_state.xml tool_dependencies.xml visualisation/ob_depiction_svg.xml
diffstat 4 files changed, 20 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/modify/ob_genProp.xml	Tue Mar 26 14:49:44 2013 -0400
+++ b/modify/ob_genProp.xml	Wed Mar 27 15:25:33 2013 -0400
@@ -30,9 +30,9 @@
     </conditional>
   </inputs>
   <outputs>
-    <data format="tabular" name="outfile">
+    <data format="tabular" name="outfile" label="${tool.name} on ${on_string}">
         <change_format>
-            <when input="$output_opts.output_format_types" value="sdf" format="sdf"/>
+            <when input="output_opts.output_format_types" value="sdf" format="sdf"/>
         </change_format>
     </data>
   </outputs>
--- a/modify/remove_protonation_state.xml	Tue Mar 26 14:49:44 2013 -0400
+++ b/modify/remove_protonation_state.xml	Wed Mar 27 15:25:33 2013 -0400
@@ -12,7 +12,7 @@
         <param name="infile" type="data" format="sdf,smi,mol,inchi" label="Molecule file" help="Dataset missing? See TIP below"/>
     </inputs>
     <outputs>
-    <data format="smi" name="outfile"/>
+        <data format_source="infile" name="outfile" />
     </outputs>
     <tests>
         <test>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Mar 27 15:25:33 2013 -0400
@@ -0,0 +1,5 @@
+<tool_dependency>
+    <package name="openbabel" version="2.3.2">
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_openbabel_2_3" owner="bgruening" changeset_revision="9e07452137da" />
+    </package>
+</tool_dependency>
--- a/visualisation/ob_depiction_svg.xml	Tue Mar 26 14:49:44 2013 -0400
+++ b/visualisation/ob_depiction_svg.xml	Wed Mar 27 15:25:33 2013 -0400
@@ -9,7 +9,7 @@
         $draw_all_carbon_atoms
         -xC 
         -O 
-        $outfile -osvg
+        $outfile -o$oformat
         #if str($sort) != "none":
             --sort $sort
         #end if
@@ -69,9 +69,19 @@
             <option value='tbonds'>Number of triple bonds</option>
             <option value='TPSA'>topological polar surface area</option>
         </param>
+
+        <param name='oformat' type='select' format='text' label="Format of the resulting picture">
+            <option value='svg'>SVG</option>
+            <option value='png'>PNG</option>
+        </param>
+
     </inputs>
     <outputs>
-        <data name="outfile" type="data" format="svg"/>
+        <data name="outfile" type="data" format="png" label="${tool.name} on ${on_string}">
+            <change_format>
+                <when input="oformat" value="svg" format="svg"/>
+            </change_format>
+        </data>
     </outputs>
     <tests>
         <test>