annotate CADDSuite-1.1/galaxyconfigs/tools/InteractionConstraintDefiner.xml @ 6:decca54699e3

Uploaded Version 1.1
author marcel
date Thu, 12 Jan 2012 11:07:03 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
1
decca54699e3 Uploaded Version 1.1
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.-->
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
3 <tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="1.1">
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
4 <description>define interaction constraint</description>
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
5 <command interpreter="bash"><![CDATA[../../InteractionConstraintDefiner
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
6 #if str( $res ) != '' and str( $res ) != 'None' :
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
7 -res "$res"
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
8 #end if
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
9 #if str( $ini ) != '' and str( $ini ) != 'None' :
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
10 -ini "$ini"
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
11 #end if
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
12 #if str( $s ) != '' and str( $s ) != 'None' :
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
13 -s "$s"
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
14 #end if
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
15 #if str( $p ) != '' and str( $p ) != 'None' :
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
16 -p "$p"
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
17 #end if
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
18 #if str( $o ) != '' and str( $o ) != 'None' :
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
19 -o "$o"
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
20 #end if
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
21 | tail -n 5
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
22 ]]></command>
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
23 <inputs>
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
24 <param name="ini" optional="true" label="input configuration file" type="data" format="ini"/>
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
25 <param name="res" optional="false" label="residue ID" area="true" type="text" size="1x15"/>
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
26 <param name="s" optional="false" label="desired minimal interation (score) between ligand and specified residue(s)" type="text" area="true" size="1x5" value="-2.0"/>
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
27 <param name="p" optional="false" label="penalty value" type="text" area="true" size="1x5" value="10"/>
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
28 </inputs>
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
29 <outputs>
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
30 <data name="o" format="ini"/>
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
31 </outputs>
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
32 <help>This tool allows to define interaction constraints for docking or scoring.
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
33
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
34 The constraint to be created will enforce a specified minimal interaction between ligands and the specified residue(s) of the receptor. Please specify residue IDs in the following manner: &lt;chain-ID&gt;:&lt;residue-ID&gt;, e.g. A:57. If you want to use more than one residue, separate their IDs by commas, e.g. A:57,B:17.
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
35
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
36 Output of this tool is a ini-file that contains the desired interaction constraint.</help>
decca54699e3 Uploaded Version 1.1
marcel
parents:
diff changeset
37 </tool>