Mercurial > repos > marcel > caddsuite_mac10_6
comparison CADDSuite-1.0.1/galaxyconfigs/tools/DockResultMerger.xml @ 5:e30a41af9d2b
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| author | marcel |
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| date | Tue, 15 Nov 2011 10:53:16 -0500 |
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| 4:af446ca2d5c6 | 5:e30a41af9d2b |
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| 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.--> | |
| 3 <tool id="dockresultmerger" name="DockResultMerger" version="1.0.1"> | |
| 4 <description>merge docking output files</description> | |
| 5 <command interpreter="bash"><![CDATA[../../DockResultMerger | |
| 6 #for $s in $series_i | |
| 7 #if str( "${s.i.file_name}" ) != '' and str( "${s.i.file_name}" ) != 'None' : | |
| 8 -i "${s.i.file_name}" | |
| 9 #end if | |
| 10 #end for | |
| 11 #if str( $o ) != '' and str( $o ) != 'None' : | |
| 12 -o "$o" | |
| 13 #end if | |
| 14 #if str( $score ) != '' and str( $score ) != 'None' : | |
| 15 -score "$score" | |
| 16 #end if | |
| 17 #if str( $min ) != '' and str( $min ) != 'None' : | |
| 18 -min "$min" | |
| 19 #end if | |
| 20 #if str( $max ) != '' and str( $max ) != 'None' : | |
| 21 -max "$max" | |
| 22 #end if | |
| 23 #if str( $k ) != '' and str( $k ) != 'None' : | |
| 24 -k "$k" | |
| 25 #end if | |
| 26 #if str( $rm ) != '' and str( $rm ) != 'None' : | |
| 27 -rm | |
| 28 #end if | |
| 29 | tail -n 5 | |
| 30 ]]></command> | |
| 31 <inputs> | |
| 32 <repeat name="series_i" title="input files" min="1"> | |
| 33 <param name="i" optional="false" label="input files" type="data" format="mol2/sdf/drf"/> | |
| 34 </repeat> | |
| 35 <param name="score" optional="true" label="Optional: score property name" area="true" type="text" size="1x15" value="score"/> | |
| 36 <param name="min" optional="true" label="Optional: minimal score value" type="text" area="true" size="1x5" value=""/> | |
| 37 <param name="max" optional="true" label="Optional: maximal score value" type="text" area="true" size="1x5" value=""/> | |
| 38 <param name="k" optional="true" label="Optional: number of output molecules" type="text" area="true" size="1x5" value=""/> | |
| 39 <param name="rm" optional="true" label="remove input files after merging" type="boolean" truevalue="true" falsevalue=""/> | |
| 40 </inputs> | |
| 41 <outputs> | |
| 42 <data name="o" format="mol2/sdf/drf" format_source="i"/> | |
| 43 </outputs> | |
| 44 <help>This tool merges and sorts molecule files as generated by docking or rescoring. | |
| 45 | |
| 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. | |
| 47 | |
| 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> | |
| 49 </tool> |