annotate CADDSuite/galaxyconfigs/tools/ProteinCheck.xml @ 0:bac3c274238f

Migrated tool version 0.93 from old tool shed archive to new tool shed repository
author marcel
date Tue, 07 Jun 2011 16:43:30 -0400
parents
children 867bf9f815a0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
1
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
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.-->
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
3 <tool id="proteincheck" name="ProteinCheck" version="0.93">
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
4 <description>quality check for proteins structures</description>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
5 <command interpreter="bash"><![CDATA[../../ProteinCheck
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
6 #if str( $i ) != '' and str( $i ) != 'None' :
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
7 -i "$i"
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
8 #end if
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
9 #if str( $o ) != '' and str( $o ) != 'None' :
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
10 -o "$o"
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
11 #end if
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
12 #if str( $bc ) != '' and str( $bc ) != 'None' :
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
13 -bc
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
14 #end if
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
15 | tail -n 5
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
16 ]]></command>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
17 <inputs>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
18 <param name="i" label="input pdb-file" optional="false" type="data" format="pdb"/>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
19 <param name="bc" label="ignore broken chains" optional="true" type="boolean" truevalue="true" falsevalue=""/>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
20 </inputs>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
21 <outputs>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
22 <data name="o" format="pdf"/>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
23 </outputs>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
24 <help>Check a given protein structure for the following errors:
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
25 * bond-lengths may not be completely senseless (i.e. &lt;0.7 or &gt;2.5 Angstroem)
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
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.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
27 * each atom must have a valid assigned element
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
28 * the protein must be protonated (since this is necessary for docking/(re-)scoring).
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
29 * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring)
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
30 * there may be no senseless temperature factors (&lt;1 or &gt;100)
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
31 * there may be no sterical clashes between atoms
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
32
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
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>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
34 </tool>