Mercurial > repos > marcel > caddsuite_mac10_6
comparison CADDSuite-1.6/galaxyconfigs/tools/PDBCutter.xml @ 8:dbb480e39d95 draft
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| author | marcel |
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| date | Sat, 15 Dec 2012 13:15:46 -0500 |
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| 7:bfab27640f5e | 8:dbb480e39d95 |
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| 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> |