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annotate CADDSuite-1.0.1/galaxyconfigs/tools/DockResultMerger.xml @ 23:389056b8864a

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Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
author greg
date Mon, 14 Nov 2011 17:02:30 -0500
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23
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
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1
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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="dockresultmerger" name="DockResultMerger" version="1.0.1">
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4 <description>merge docking output files</description>
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5 <command interpreter="bash"><![CDATA[../../DockResultMerger
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6 #for $s in $series_i
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7 #if str( "${s.i.file_name}" ) != '' and str( "${s.i.file_name}" ) != 'None' :
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8 -i "${s.i.file_name}"
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9 #end if
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10 #end for
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11 #if str( $o ) != '' and str( $o ) != 'None' :
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12 -o "$o"
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13 #end if
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14 #if str( $score ) != '' and str( $score ) != 'None' :
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15 -score "$score"
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16 #end if
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17 #if str( $min ) != '' and str( $min ) != 'None' :
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18 -min "$min"
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19 #end if
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20 #if str( $max ) != '' and str( $max ) != 'None' :
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21 -max "$max"
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22 #end if
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23 #if str( $k ) != '' and str( $k ) != 'None' :
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24 -k "$k"
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25 #end if
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26 #if str( $rm ) != '' and str( $rm ) != 'None' :
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27 -rm
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28 #end if
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29 | tail -n 5
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30 ]]></command>
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31 <inputs>
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32 <repeat name="series_i" title="input files" min="1">
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33 <param name="i" optional="false" label="input files" type="data" format="mol2/sdf/drf"/>
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34 </repeat>
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35 <param name="score" optional="true" label="Optional: score property name" area="true" type="text" size="1x15" value="score"/>
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36 <param name="min" optional="true" label="Optional: minimal score value" type="text" area="true" size="1x5" value=""/>
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37 <param name="max" optional="true" label="Optional: maximal score value" type="text" area="true" size="1x5" value=""/>
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38 <param name="k" optional="true" label="Optional: number of output molecules" type="text" area="true" size="1x5" value=""/>
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39 <param name="rm" optional="true" label="remove input files after merging" type="boolean" truevalue="true" falsevalue=""/>
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40 </inputs>
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41 <outputs>
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42 <data name="o" format="mol2/sdf/drf" format_source="i"/>
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43 </outputs>
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44 <help>This tool merges and sorts molecule files as generated by docking or rescoring.
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45
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46 You need to specify the property-tag name of the scores according to which the molecules should be sorted. Optionally you can filter those compounds that were assigned a score above and/or below specified thresholds. If desired, you can furthermore choose to have only the compounds with the k best scores written to the output file.
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47
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48 Output of DockResultMerger is one molecule containing the molecules found in input-files (that matched all filter criteria, if any), sorted ascendingly according to their scores.</help>
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49 </tool>