annotate galaxy_stubs/ProteinCheck.xml @ 2:605370bc1def draft default tip

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<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
<!--Proposed Tool Section: [Checks and evaluations]-->
<tool id="ProteinCheck" name="ProteinCheck" version="1.1.0">
  <description>quality check for proteins structures</description>
  <macros>
    <token name="@EXECUTABLE@">ProteinCheck</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>ProteinCheck

#if $param_i:
  -i $param_i
#end if
#if $param_o:
  -o $param_o
#end if
#if $param_bc:
  -bc $param_bc
#end if
</command>
  <inputs>
    <param name="param_i" type="data" format="pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input pdb-file" help="(-i) "/>
    <param name="param_bc" type="integer" min="0" max="1" optional="True" value="0" label="ignore broken chains" help="(-bc) "/>
  </inputs>
  <expand macro="advanced_options"/>
  <outputs>
    <data name="param_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>