diff CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml @ 4:af446ca2d5c6

Uploaded

--- a/CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml	Fri Sep 02 08:54:17 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.95">
+<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.9.6">
     <description>generate 3D coordinates for small molecules</description>
     <command interpreter="bash"><![CDATA[../../Ligand3DGenerator 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -12,11 +12,15 @@
 #if str( $ph ) != ''  and str( $ph ) != 'None' :
    -ph "$ph"
 #end if
+#if str( $rm ) != ''  and str( $rm ) != 'None' :
+   -rm
+#end if
  | tail -n 5
 ]]></command>
     <inputs>
         <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/>
         <param name="ph" optional="true" label="Optional: pH-value for pH-dep. protonation" type="text" area="true" size="1x5" value="7.0"/>
+        <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/>
     </inputs>
     <outputs>
         <data name="o" format="mol2/sdf/drf" format_source="i"/>
@@ -26,5 +30,5 @@
 
 Note however, that the main purpose of this tool is to generate feasible start-conformations for docking or other optimization procedures. Therefore, the generated 3D coordinates for each fragment should be all right, but in extreme cases (i.e. very large and/or complex molecules) different fragments might still overlap with each other.
 
-Supported formats are mol2, sdf, drf, pdb, ac, ent, brk, hin, mol, xyz.</help>
+Supported formats are mol2, sdf, drf, pdb, ac, ent, brk, hin, mol, xyz, mol2.gz, sdf.gz, drf.gz, pdb.gz, ac.gz, ent.gz, brk.gz, hin.gz, mol.gz, xyz.gz.</help>
 </tool>
\ No newline at end of file