comparison CADDSuite/galaxyconfigs/tools/PDBCutter.xml @ 3:ff6df146c0d5

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author marcel
date Sun, 26 Jun 2011 13:53:57 -0400
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2:bbc4a2c1d276 3:ff6df146c0d5
1
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.-->
3 <tool id="pdbcutter" name="PDBCutter" version="0.94">
4 <description>separate ligand and receptor</description>
5 <command interpreter="bash"><![CDATA[../../PDBCutter
6 #if str( $i ) != '' and str( $i ) != 'None' :
7 -i "$i"
8 #end if
9 #if str( $rec ) != '' and str( $rec ) != 'None' :
10 -rec "$rec"
11 #end if
12 #if str( $lig ) != '' and str( $lig ) != 'None' :
13 -lig "$lig"
14 #end if
15 #if str( $lig_chain ) != '' and str( $lig_chain ) != 'None' :
16 -lig_chain "$lig_chain"
17 #end if
18 #if str( $lig_name ) != '' and str( $lig_name ) != 'None' :
19 -lig_name "$lig_name"
20 #end if
21 #if str( $rm_ch ) != '' and str( $rm_ch ) != 'None' :
22 -rm_ch "$rm_ch"
23 #end if
24 #if str( $rm_res ) != '' and str( $rm_res ) != 'None' :
25 -rm_res "$rm_res"
26 #end if
27 | tail -n 5
28 ]]></command>
29 <inputs>
30 <param name="i" label="input pdb-file" optional="false" type="data" format="pdb"/>
31 <param name="lig_chain" label="chain-name of ligand" optional="false" area="true" type="text" size="1x15"/>
32 <param name="lig_name" label="ligand name" optional="false" area="true" type="text" size="1x15"/>
33 <param name="rm_ch" label="protein chains that are to be deleted" optional="true" area="true" type="text" size="1x15"/>
34 <param name="rm_res" label="pdb-residues that are to be deleted (e.g. water or ions)" optional="true" area="true" type="text" size="1x15"/>
35 </inputs>
36 <outputs>
37 <data name="rec" format="pdb"/>
38 <data name="lig" format="pdb"/>
39 </outputs>
40 <help>This tool splits a given pdb-file into two files containing receptor and reference ligand, respectively.
41
42 The name of the reference ligand (exactly as it appears in the pdb-file) and the name of its chain need to be specified by '-lig_name' and '-lig_chain'.
43 Optionally, chains (e.g. in case of multimers) or pdb-residues (e.g. water or ions) that you don't need can be deleted from the receptor. In this case, specify their names with '-rm_ch' or '-rm_res'.
44
45 Output of this tool is one pdb-file containing the receptor-structure, i.e. the protein w/o reference ligand and w/o undesired chains/residues (if any were specified), and one pdb-file containing the reference ligand.</help>
46 </tool>