Mercurial > repos > marcel > caddsuite_mac10_6
diff CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml @ 4:af446ca2d5c6
Uploaded
author | marcel |
---|---|
date | Fri, 02 Sep 2011 08:54:17 -0400 |
parents | bb26168c5715 |
children |
line wrap: on
line diff
--- 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