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comparison CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml @ 8:9ab6da6cd36c

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author marcel
date Fri, 02 Sep 2011 08:48:21 -0400
parents 5b29b679ee6d
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7:5b29b679ee6d 8:9ab6da6cd36c
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="ligand3dgenerator" name="Ligand3DGenerator" version="0.95"> 3 <tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.9.6">
4 <description>generate 3D coordinates for small molecules</description> 4 <description>generate 3D coordinates for small molecules</description>
5 <command interpreter="bash"><![CDATA[../../Ligand3DGenerator 5 <command interpreter="bash"><![CDATA[../../Ligand3DGenerator
6 #if str( $i ) != '' and str( $i ) != 'None' : 6 #if str( $i ) != '' and str( $i ) != 'None' :
7 -i "$i" 7 -i "$i"
8 #end if 8 #end if
10 -o "$o" 10 -o "$o"
11 #end if 11 #end if
12 #if str( $ph ) != '' and str( $ph ) != 'None' : 12 #if str( $ph ) != '' and str( $ph ) != 'None' :
13 -ph "$ph" 13 -ph "$ph"
14 #end if 14 #end if
15 #if str( $rm ) != '' and str( $rm ) != 'None' :
16 -rm
17 #end if
15 | tail -n 5 18 | tail -n 5
16 ]]></command> 19 ]]></command>
17 <inputs> 20 <inputs>
18 <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/> 21 <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/>
19 <param name="ph" optional="true" label="Optional: pH-value for pH-dep. protonation" type="text" area="true" size="1x5" value="7.0"/> 22 <param name="ph" optional="true" label="Optional: pH-value for pH-dep. protonation" type="text" area="true" size="1x5" value="7.0"/>
23 <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/>
20 </inputs> 24 </inputs>
21 <outputs> 25 <outputs>
22 <data name="o" format="mol2/sdf/drf" format_source="i"/> 26 <data name="o" format="mol2/sdf/drf" format_source="i"/>
23 </outputs> 27 </outputs>
24 <help>This tool generates 3D conformations for small molecules and adds hydrogens to them. 28 <help>This tool generates 3D conformations for small molecules and adds hydrogens to them.
25 As input we only a chemical file containing valid topologies. Any 2D or 3D conformations in the input file are ignored, but the existence of the correct bond-orders is necessary. 29 As input we only a chemical file containing valid topologies. Any 2D or 3D conformations in the input file are ignored, but the existence of the correct bond-orders is necessary.
26 30
27 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. 31 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.
28 32
29 Supported formats are mol2, sdf, drf, pdb, ac, ent, brk, hin, mol, xyz.</help> 33 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>
30 </tool> 34 </tool>