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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_stubs/ProteinCheck.xml	Tue Jul 12 12:33:33 2016 -0400
@@ -0,0 +1,44 @@
+<?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>