Mercurial > repos > marcel > caddsuite_linux_x86_64
comparison CADDSuite-1.6/galaxyconfigs/tools/LigCheck.xml @ 17:25a03362403c draft
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| author | marcel |
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| date | Sat, 15 Dec 2012 13:10:41 -0500 |
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| 16:1a24aef40d01 | 17:25a03362403c |
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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="ligcheck" name="LigCheck" version="1.6"> | |
| 4 <description>check molecules for errors</description> | |
| 5 <command interpreter="bash"><![CDATA[../../LigCheck | |
| 6 #if str( $i ) != '' and str( $i ) != 'None' : | |
| 7 -i "$i" | |
| 8 #end if | |
| 9 #if str( $o ) != '' and str( $o ) != 'None' : | |
| 10 -o "$o" | |
| 11 #end if | |
| 12 #if str( $ef ) != '' and str( $ef ) != 'None' : | |
| 13 -ef "$ef" | |
| 14 #end if | |
| 15 #if str( $ri ) != '' and str( $ri ) != 'None' : | |
| 16 -ri | |
| 17 #end if | |
| 18 #if str( $ut ) != '' and str( $ut ) != 'None' : | |
| 19 -ut | |
| 20 #end if | |
| 21 #if str( $nc ) != '' and str( $nc ) != 'None' : | |
| 22 -nc | |
| 23 #end if | |
| 24 #if str( $rm ) != '' and str( $rm ) != 'None' : | |
| 25 -rm | |
| 26 #end if | |
| 27 | tail -n 5 | |
| 28 ]]></command> | |
| 29 <inputs> | |
| 30 <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/> | |
| 31 <param name="ef" optional="true" label="Optional: error fraction; print error if fraction of invalid mols is larger" type="text" area="true" size="1x5" value="0.5"/> | |
| 32 <param name="ri" optional="true" label="remove invalid molecules." type="boolean" truevalue="true" falsevalue="" checked="true"/> | |
| 33 <param name="ut" optional="true" label="check for unique topologies" type="boolean" truevalue="true" falsevalue=""/> | |
| 34 <param name="nc" optional="true" label="no not check for unique conformations" type="boolean" truevalue="true" falsevalue=""/> | |
| 35 <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/> | |
| 36 </inputs> | |
| 37 <outputs> | |
| 38 <data name="o" format="mol2/sdf/drf" format_source="i"/> | |
| 39 </outputs> | |
| 40 <help>This tool checks all molecules of the given input file for errors. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). | |
| 41 | |
| 42 The following checks are done for each molecule: | |
| 43 | |
| 44 * bond-lengths may not be completely senseless (i.e. <0.7 or >2.5 Angstroem) | |
| 45 * each 'molecule' in the input file may only contain one actual molecule, i.e. there may be no unconnected atoms or fragments. | |
| 46 * each atom must have a valid assigned element | |
| 47 * the molecule must be protonated (since this is necessary for docking/(re-)scoring). | |
| 48 * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring) | |
| 49 * partial charges may not contain completely senseless values (>5 or <-5). | |
| 50 * each conformation should appear only once within the given file, otherwise it is rejected and not written to the output file. However, if option '-ut' is used, molecules will instead be checked for unique topologies. | |
| 51 | |
| 52 If option '-ri' is used, only those molecules that pass all those tests are written to the output file. If this option is not used, all molecules are written to output containing a property 'score_ligcheck' with a value of 1 if the molecule passed all tests or with a value of 0 if it did not pass them.</help> | |
| 53 </tool> |