Mercurial > repos > marcel > caddsuite_linux_x86_64
comparison CADDSuite/galaxyconfigs/tools/PDBCutter.xml @ 3:ff6df146c0d5
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| author | marcel |
|---|---|
| date | Sun, 26 Jun 2011 13:53:57 -0400 |
| parents | |
| children | b7a89b15646f |
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| 2:bbc4a2c1d276 | 3:ff6df146c0d5 |
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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="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> |