Mercurial > repos > marcel > caddsuite_linux_x86_64
comparison CADDSuite/galaxyconfigs/tools/TaGRes.xml @ 5:b7a89b15646f
Uploaded
| author | marcel |
|---|---|
| date | Tue, 12 Jul 2011 10:23:33 -0400 |
| parents | ff6df146c0d5 |
| children |
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| 4:02c8570cde57 | 5:b7a89b15646f |
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| 1 | 1 |
| 2 <!--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.--> | 2 <!--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.--> |
| 3 <tool id="tagres" name="TaGRes" version="0.94"> | 3 <tool id="tagres" name="TaGRes" version="0.95"> |
| 4 <description>Target-specific Grid-Rescoring</description> | 4 <description>Target-specific Grid-Rescoring</description> |
| 5 <command interpreter="bash"><![CDATA[../../TaGRes | 5 <command interpreter="bash"><![CDATA[../../TaGRes |
| 6 #if str( $rec ) != '' and str( $rec ) != 'None' : | 6 #if str( $rec ) != '' and str( $rec ) != 'None' : |
| 7 -rec "$rec" | 7 -rec "$rec" |
| 8 #end if | 8 #end if |
| 16 -i "$i" | 16 -i "$i" |
| 17 #end if | 17 #end if |
| 18 #if str( $mod ) != '' and str( $mod ) != 'None' : | 18 #if str( $mod ) != '' and str( $mod ) != 'None' : |
| 19 -mod "$mod" | 19 -mod "$mod" |
| 20 #end if | 20 #end if |
| 21 #if str( $tf ) != '' and str( $tf ) != 'None' : | |
| 22 -tf "$tf" | |
| 23 #end if | |
| 21 #if str( $o ) != '' and str( $o ) != 'None' : | 24 #if str( $o ) != '' and str( $o ) != 'None' : |
| 22 -o "$o" | 25 -o "$o" |
| 23 #end if | 26 #end if |
| 24 #if str( $method ) != '' and str( $method ) != 'None' : | 27 #if str( $method ) != '' and str( $method ) != 'None' : |
| 25 -method "$method" | 28 -method "$method" |
| 28 -function "$function" | 31 -function "$function" |
| 29 #end if | 32 #end if |
| 30 | tail -n 5 | 33 | tail -n 5 |
| 31 ]]></command> | 34 ]]></command> |
| 32 <inputs> | 35 <inputs> |
| 33 <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/> | 36 <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/> |
| 34 <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/> | 37 <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/> |
| 35 <param name="ini" label="configuration file" optional="true" type="data" format="ini"/> | 38 <param name="ini" optional="true" label="configuration file" type="data" format="ini"/> |
| 36 <param name="i" label="compounds to be rescored" optional="false" type="data" format="mol2/sdf/drf"/> | 39 <param name="i" optional="false" label="compounds to be rescored" type="data" format="mol2/sdf/drf"/> |
| 37 <param name="mod" label="model-file generated by TaGRes-train" optional="false" type="data" format="data"/> | 40 <param name="mod" optional="false" label="model-file generated by TaGRes-train" type="data" format="data"/> |
| 38 <param name="method" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" optional="false" type="select"> | 41 <param name="tf" optional="true" label="Optional: top-scored fraction of compounds not to be rescored" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/> |
| 42 <param name="method" optional="false" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" type="select"> | |
| 39 <option value="Rescoring3D">Rescoring3D</option> | 43 <option value="Rescoring3D">Rescoring3D</option> |
| 40 <option value="Rescoring4D">Rescoring4D</option> | 44 <option value="Rescoring4D">Rescoring4D</option> |
| 41 <option value="Rescoring1D">Rescoring1D</option> | 45 <option value="Rescoring1D">Rescoring1D</option> |
| 42 </param> | 46 </param> |
| 43 <param name="function" label="scoring function: 'MM' or 'PLP'" optional="true" type="select"> | 47 <param name="function" optional="true" label="scoring function: 'MM' or 'PLP'" type="select"> |
| 44 <option value="MM">MM</option> | 48 <option value="MM">MM</option> |
| 45 <option value="PLP">PLP</option> | 49 <option value="PLP">PLP</option> |
| 46 </param> | 50 </param> |
| 47 </inputs> | 51 </inputs> |
| 48 <outputs> | 52 <outputs> |