<!--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.-->
<tool id="proteincheck" name="ProteinCheck" version="1.0.1">
    <description>quality check for proteins structures</description>
    <command interpreter="bash"><![CDATA[../../ProteinCheck 
#if str( $i ) != ''  and str( $i ) != 'None' :
   -i "$i"
#end if
#if str( $o ) != ''  and str( $o ) != 'None' :
   -o "$o"
#end if
#if str( $bc ) != ''  and str( $bc ) != 'None' :
   -bc
#end if
 | tail -n 5
]]></command>
    <inputs>
        <param name="i" optional="false" label="input pdb-file" type="data" format="pdb"/>
        <param name="bc" optional="true" label="ignore broken chains" type="boolean" truevalue="true" falsevalue=""/>
    </inputs>
    <outputs>
        <data name="o" format="pdf"/>
    </outputs>
    <help>Check a given protein structure for the following errors:
    * bond-lengths may not be completely senseless (i.e. &lt;0.7 or &gt;2.5 Angstroem)
    * 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.
    * each atom must have a valid assigned element
    * the protein must be protonated (since this is necessary for docking/(re-)scoring).
    * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring)
    * there may be no senseless temperature factors (&lt;1 or &gt;100)
    * there may be no sterical clashes between atoms

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>
</tool>