Mercurial > repos > marcel > caddsuite_mac10_6

annotate CADDSuite-1.5/galaxyconfigs/tools/LigCheck.xml @ 7:bfab27640f5e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
CADDSuite version 1.5
author Marcel Schumann <schumann.marcel@gmail.com>
date Tue, 24 Jul 2012 11:13:59 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
1
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
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.-->
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
3 <tool id="ligcheck" name="LigCheck" version="1.5">
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
4 <description>check molecules for errors</description>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
5 <command interpreter="bash"><![CDATA[../../LigCheck
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
6 #if str( $i ) != '' and str( $i ) != 'None' :
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
7 -i "$i"
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
8 #end if
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
9 #if str( $o ) != '' and str( $o ) != 'None' :
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
10 -o "$o"
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
11 #end if
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
12 #if str( $ef ) != '' and str( $ef ) != 'None' :
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
13 -ef "$ef"
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
14 #end if
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
15 #if str( $ri ) != '' and str( $ri ) != 'None' :
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
16 -ri
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
17 #end if
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
18 #if str( $ut ) != '' and str( $ut ) != 'None' :
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
19 -ut
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
20 #end if
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
21 #if str( $nc ) != '' and str( $nc ) != 'None' :
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
22 -nc
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
23 #end if
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
24 #if str( $rm ) != '' and str( $rm ) != 'None' :
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
25 -rm
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
26 #end if
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
27 | tail -n 5
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
28 ]]></command>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
29 <inputs>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
30 <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
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"/>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
32 <param name="ri" optional="true" label="remove invalid molecules." type="boolean" truevalue="true" falsevalue="" checked="true"/>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
33 <param name="ut" optional="true" label="check for unique topologies" type="boolean" truevalue="true" falsevalue=""/>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
34 <param name="nc" optional="true" label="no not check for unique conformations" type="boolean" truevalue="true" falsevalue=""/>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
35 <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
36 </inputs>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
37 <outputs>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
38 <data name="o" format="mol2/sdf/drf" format_source="i"/>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
39 </outputs>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
40 <help>This tool checks all molecules of the given input file for errors. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
41
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
42 The following checks are done for each molecule:
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
43
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
44 * bond-lengths may not be completely senseless (i.e. &lt;0.7 or &gt;2.5 Angstroem)
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
45 * each 'molecule' in the input file may only contain one actual molecule, i.e. there may be no unconnected atoms or fragments.
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
46 * each atom must have a valid assigned element
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
47 * the molecule must be protonated (since this is necessary for docking/(re-)scoring).
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
48 * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring)
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
49 * partial charges may not contain completely senseless values (&gt;5 or &lt;-5).
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
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.
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
51
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
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>
bfab27640f5e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
53 </tool>