comparison CADDSuite-1.6/galaxyconfigs/tools/PDBCutter.xml @ 8:dbb480e39d95 draft

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author marcel
date Sat, 15 Dec 2012 13:15:46 -0500
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7:bfab27640f5e 8:dbb480e39d95
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="1.6">
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( $id ) != '' and str( $id ) != 'None' :
25 -id "$id"
26 #end if
27 #if str( $p ) != '' and str( $p ) != 'None' :
28 -p "$p"
29 #end if
30 #if str( $rm_res ) != '' and str( $rm_res ) != 'None' :
31 -rm_res "$rm_res"
32 #end if
33 #if str( $auto ) != '' and str( $auto ) != 'None' :
34 -auto
35 #end if
36 | tail -n 5
37 ]]></command>
38 <inputs>
39 <param name="i" optional="false" label="input pdb-file" type="data" format="pdb"/>
40 <param name="lig_chain" optional="false" label="chain-name of ligand" area="true" type="text" size="1x15"/>
41 <param name="lig_name" optional="false" label="ligand name" area="true" type="text" size="1x15"/>
42 <param name="rm_ch" optional="true" label="Optional: protein chains that are to be deleted" area="true" type="text" size="1x15"/>
43 <param name="id" optional="true" label="Optional: PDB ID for download of ligand as sdf from PDB server, if desired" area="true" type="text" size="1x15"/>
44 <param name="p" optional="true" label="Optional: proxy for ligand download, if required" area="true" type="text" size="1x15"/>
45 <param name="rm_res" optional="true" label="Optional: pdb-residues that are to be deleted (e.g. water or ions)" area="true" type="text" size="1x15"/>
46 <param name="auto" optional="true" label="extract largest heterosystem as ligand (ignore specified lig. def.)" type="boolean" truevalue="true" falsevalue=""/>
47 </inputs>
48 <outputs>
49 <data name="rec" format="pdb"/>
50 <data name="lig" format="pdb"/>
51 </outputs>
52 <help>This tool splits a given pdb-file into two files containing receptor and reference ligand, respectively.
53
54 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'.
55 If desired, the correct topology of the reference ligand can be downloaded by this tool from the Protein Data Bank as an sd-file and stored in the specified ligand output file.
56 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'.
57
58 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 file containing the reference ligand.</help>
59 </tool>