Mercurial > repos > marcel > caddsuite_linux_x86_64
annotate CADDSuite-1.5/galaxyconfigs/tools/AntitargetRescorer.xml @ 16:1a24aef40d01 draft
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author | marcel |
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date | Tue, 24 Jul 2012 11:10:07 -0400 |
parents | ac342506cd4e |
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CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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1 |
ac342506cd4e
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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.--> |
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3 <tool id="antitargetrescorer" name="AntitargetRescorer" version="1.5"> |
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4 <description>rescore w/ anti-target dock-results</description> |
ac342506cd4e
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5 <command interpreter="bash"><![CDATA[../../AntitargetRescorer |
ac342506cd4e
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6 #if str( $t ) != '' and str( $t ) != 'None' : |
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7 -t "$t" |
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8 #end if |
ac342506cd4e
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9 #if str( $at ) != '' and str( $at ) != 'None' : |
ac342506cd4e
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10 -at "$at" |
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11 #end if |
ac342506cd4e
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12 #if str( $o ) != '' and str( $o ) != 'None' : |
ac342506cd4e
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13 -o "$o" |
ac342506cd4e
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14 #end if |
ac342506cd4e
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15 | tail -n 5 |
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16 ]]></command> |
ac342506cd4e
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17 <inputs> |
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18 <param name="t" optional="false" label="input file w/ target dock-results" type="data" format="mol2/sdf/drf"/> |
ac342506cd4e
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19 <param name="at" optional="false" label="input file w/ anti-target dock-results" type="data" format="mol2/sdf/drf"/> |
ac342506cd4e
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20 </inputs> |
ac342506cd4e
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21 <outputs> |
ac342506cd4e
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22 <data name="o" format="mol2/sdf/drf" format_source="t"/> |
ac342506cd4e
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23 </outputs> |
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24 <help>This tool rescores docking output poses. |
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25 AntitargetRescoring can be used to try to enhance target specificity. Therefore, dock your compounds into your target of interest and into a (very) different protein and supply the docking results here. All compounds that received a very good antitarget-score will thus be penalized, i.e. they will have a much worse score within the output file. |
ac342506cd4e
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26 |
ac342506cd4e
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27 As input we need: |
ac342506cd4e
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28 * a file containing the compounds that are to be rescored. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). Those compound should have been docket into the specified protein (i.e. the target). |
ac342506cd4e
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29 * a file containing the same compounds docked into the antitarget. |
ac342506cd4e
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Marcel Schumann <schumann.marcel@gmail.com>
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30 |
ac342506cd4e
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31 Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 'antitarget_rescore'.</help> |
ac342506cd4e
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32 </tool> |