Mercurial > repos > marcel > caddsuite_linux_x86_64

annotate CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml @ 1:867bf9f815a0

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author g2cmnty@test-web1.g2.bx.psu.edu
date Sun, 26 Jun 2011 13:45:14 -0400
parents bac3c274238f
children
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.-->
1
867bf9f815a0 Uploaded
g2cmnty@test-web1.g2.bx.psu.edu
parents: 0
diff changeset
3 <tool id="rmsdcalculator" name="RMSDCalculator" version="0.94">
0
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
4 <description>calculate RMSD between poses</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[../../RMSDCalculator
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( $org ) != '' and str( $org ) != 'None' :
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
10 -org "$org"
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( $o ) != '' and str( $o ) != 'None' :
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
13 -o "$o"
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 -quiet
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
16 | tail -n 5
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
17 ]]></command>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
18 <inputs>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
19 <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
20 <param name="org" label="molecule file containing the original ('true') poses" optional="false" type="data" format="mol2/sdf/drf"/>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
21 </inputs>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
22 <outputs>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
23 <data name="o" format="mol2/sdf/drf" format_source="i"/>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
24 </outputs>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
25 <help>This tool calculates the RMSD between different conformations of the same molecule.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
26
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
27 Therefore this tool can for example be used to evaluate the different between ligands taken from co-crystal structures and their poses generated by a docking.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
28 Molecules may be sorted differently in the two input files; a topology hashkey will be used to match molecules to each other.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
29
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
30 Output of this tool is a molecule file which will for each molecule contain a property-tag 'RMSD' holding the calculated RMSD value.</help>
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
marcel
parents:
diff changeset
31 </tool>