|
14
|
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="proteincheck" name="ProteinCheck" version="1.1">
|
|
|
4 <description>quality check for proteins structures</description>
|
|
|
5 <command interpreter="bash"><![CDATA[../../ProteinCheck
|
|
|
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( $bc ) != '' and str( $bc ) != 'None' :
|
|
|
13 -bc
|
|
|
14 #end if
|
|
|
15 | tail -n 5
|
|
|
16 ]]></command>
|
|
|
17 <inputs>
|
|
|
18 <param name="i" optional="false" label="input pdb-file" type="data" format="pdb"/>
|
|
|
19 <param name="bc" optional="true" label="ignore broken chains" type="boolean" truevalue="true" falsevalue=""/>
|
|
|
20 </inputs>
|
|
|
21 <outputs>
|
|
|
22 <data name="o" format="pdf"/>
|
|
|
23 </outputs>
|
|
|
24 <help>Check a given protein structure for the following errors:
|
|
|
25 * bond-lengths may not be completely senseless (i.e. <0.7 or >2.5 Angstroem)
|
|
|
26 * each chain may only contain one actual molecule, i.e. there may be no unconnected atoms or fragments. This test is skipped if the above box is checked.
|
|
|
27 * each atom must have a valid assigned element
|
|
|
28 * the protein must be protonated (since this is necessary for docking/(re-)scoring).
|
|
|
29 * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring)
|
|
|
30 * there may be no senseless temperature factors (<1 or >100)
|
|
|
31 * there may be no sterical clashes between atoms
|
|
|
32
|
|
|
33 A protein structure quality report, containing the results of those tests and a secondary structure prediction, a Ramachandran plot and a temperature factor plot will be generated and saved as a pdf-file.</help>
|
|
|
34 </tool> |
