comparison CADDSuite-1.0/galaxyconfigs/tools/ProteinCheck.xml @ 14:55c32b55c2c2

Uploaded Version 1.1
author marcel
date Thu, 12 Jan 2012 11:00:43 -0500
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13:cce3667779c2 14:55c32b55c2c2
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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. &lt;0.7 or &gt;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 (&lt;1 or &gt;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>