Mercurial > repos > marcel > caddsuite_linux_x86_64

comparison CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml @ 5:b7a89b15646f

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author marcel
date Tue, 12 Jul 2011 10:23:33 -0400
parents ff6df146c0d5
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4:02c8570cde57 5:b7a89b15646f
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="combilibgenerator" name="CombiLibGenerator" version="0.94"> 3 <tool id="combilibgenerator" name="CombiLibGenerator" version="0.95">
4 <description>generate combinatorial lib</description> 4 <description>generate combinatorial lib</description>
5 <command interpreter="bash"><![CDATA[../../CombiLibGenerator 5 <command interpreter="bash"><![CDATA[../../CombiLibGenerator
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 | tail -n 5 12 | tail -n 5
13 ]]></command> 13 ]]></command>
14 <inputs> 14 <inputs>
15 <param name="i" label="input combi-lib file" optional="false" type="data" format="data"/> 15 <param name="i" optional="false" label="input combi-lib file" type="data" format="data"/>
16 </inputs> 16 </inputs>
17 <outputs> 17 <outputs>
18 <data name="o" format="mol2/sdf/drf"/> 18 <data name="o" format="mol2/sdf/drf"/>
19 </outputs> 19 </outputs>
20 <help>This tool generates a combinatorial library by combining the given molecule scaffolds with possible combinations of moieties. 20 <help>This tool generates a combinatorial library by combining the given molecule scaffolds with possible combinations of moieties.
21 21
22 As input we need a text file specifying SMARTS expressions for the desired scaffolds and R-groups. Its format should look like the following example, although you may specify as many scaffolds and as many SMARTS expressions per R-group as you need: 22 As input we need a text file specifying SMARTS expressions for the desired scaffolds and R-groups. Its format should look like the following example, although you may specify as many scaffolds and as many SMARTS expressions per R-group as you need:
23 23
24 &lt;scaffold&gt; 24 &lt;scaffold&gt;
25 Fc1ccc(cc1)C2=C(C([R1])=NO2)c3ccnc([R2])c3 25 Fc1ccc(cc1)C2=C(C([R1])=NO2)c3ccnc([R2])c3
26 Fc1ccc(cc1)C2=NOC([R1])=C2cccnc([R2])c3
27 &lt;moietyR1&gt; 26 &lt;moietyR1&gt;
28 [R1]C(C)(C)C 27 [R1]C(C)(C)C
29 &lt;moietyR2&gt; 28 &lt;moietyR2&gt;
30 [R2]OC(C)(C)C 29 [R2]OC(C)(C)C
31 30