Mercurial > repos > marcel > caddsuite_linux_x86_64
comparison CADDSuite-1.5/galaxyconfigs/tools/DBImporter.xml @ 15:ac342506cd4e draft
CADDSuite version 1.5
| author | Marcel Schumann <schumann.marcel@gmail.com> |
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| date | Tue, 24 Jul 2012 11:08:49 -0400 |
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| 14:55c32b55c2c2 | 15:ac342506cd4e |
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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="dbimporter" name="DBImporter" version="1.5 (ob)"> | |
| 4 <description>import molecules into data base</description> | |
| 5 <command interpreter="bash"><![CDATA[../../DBImporter | |
| 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( $target ) != '' and str( $target ) != 'None' : | |
| 13 -target "$target" | |
| 14 #end if | |
| 15 #if str( $d ) != '' and str( $d ) != 'None' : | |
| 16 -d "$d" | |
| 17 #end if | |
| 18 #if str( $u ) != '' and str( $u ) != 'None' : | |
| 19 -u "$u" | |
| 20 #end if | |
| 21 #if str( $h ) != '' and str( $h ) != 'None' : | |
| 22 -h "$h" | |
| 23 #end if | |
| 24 #if str( $port ) != '' and str( $port ) != 'None' : | |
| 25 -port "$port" | |
| 26 #end if | |
| 27 #if str( $p ) != '' and str( $p ) != 'None' : | |
| 28 -p "$p" | |
| 29 #end if | |
| 30 #if str( $vn ) != '' and str( $vn ) != 'None' : | |
| 31 -vn "$vn" | |
| 32 #end if | |
| 33 #if str( $vid ) != '' and str( $vid ) != 'None' : | |
| 34 -vid "$vid" | |
| 35 #end if | |
| 36 #if str( $vd ) != '' and str( $vd ) != 'None' : | |
| 37 -vd "$vd" | |
| 38 #end if | |
| 39 #if str( $vu ) != '' and str( $vu ) != 'None' : | |
| 40 -vu "$vu" | |
| 41 #end if | |
| 42 #if str( $run_clustering ) != '' and str( $run_clustering ) != 'None' : | |
| 43 -run_clustering | |
| 44 #end if | |
| 45 | tail -n 5 | |
| 46 ]]></command> | |
| 47 <inputs> | |
| 48 <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/> | |
| 49 <param name="target" optional="true" label="Optional: target/dataset name whose molecules should be exported" area="true" type="text" size="1x15"/> | |
| 50 <param name="d" optional="false" label="database name" area="true" type="text" size="1x15"/> | |
| 51 <param name="u" optional="false" label="database username" area="true" type="text" size="1x15"/> | |
| 52 <param name="h" optional="false" label="database host" area="true" type="text" size="1x15"/> | |
| 53 <param name="port" optional="true" label="Optional: database port" type="text" area="true" size="1x5" value="3306"/> | |
| 54 <param name="p" optional="false" label="database password" area="true" type="text" size="1x15"/> | |
| 55 <param name="vn" optional="true" label="Optional: name of compound vendor" area="true" type="text" size="1x15"/> | |
| 56 <param name="vid" optional="true" label="Optional: name of vendor's compound-ID tag in sd-file" area="true" type="text" size="1x15"/> | |
| 57 <param name="vd" optional="true" label="Optional: vendor library date or version" area="true" type="text" size="1x15"/> | |
| 58 <param name="vu" optional="true" label="Optional: url from wich vendor library was obtained" area="true" type="text" size="1x15"/> | |
| 59 <param name="run_clustering" optional="true" label="cluster entire database after importing compounds" type="boolean" truevalue="true" falsevalue=""/> | |
| 60 </inputs> | |
| 61 <outputs> | |
| 62 <data name="o" format="txt"/> | |
| 63 </outputs> | |
| 64 <help>This tool imports molecules into a database. | |
| 65 As input we need the file containing the molecules to be imported in sd-, mol2- or drf-format.</help> | |
| 66 </tool> |