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annotate CADDSuite/galaxyconfigs/tools/PDBCutter.xml @ 0:bac3c274238f

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Migrated tool version 0.93 from old tool shed archive to new tool shed repository
author marcel
date Tue, 07 Jun 2011 16:43:30 -0400
parents
children 867bf9f815a0
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bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
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1
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository
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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.-->
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3 <tool id="pdbcutter" name="PDBCutter" version="0.93">
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4 <description>separate ligand and receptor</description>
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5 <command interpreter="bash"><![CDATA[../../PDBCutter
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6 #if str( $i ) != '' and str( $i ) != 'None' :
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7 -i "$i"
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8 #end if
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9 #if str( $rec ) != '' and str( $rec ) != 'None' :
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10 -rec "$rec"
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11 #end if
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12 #if str( $lig ) != '' and str( $lig ) != 'None' :
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13 -lig "$lig"
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14 #end if
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15 #if str( $lig_chain ) != '' and str( $lig_chain ) != 'None' :
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16 -lig_chain "$lig_chain"
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17 #end if
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18 #if str( $lig_name ) != '' and str( $lig_name ) != 'None' :
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19 -lig_name "$lig_name"
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20 #end if
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21 #if str( $rm_ch ) != '' and str( $rm_ch ) != 'None' :
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22 -rm_ch "$rm_ch"
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23 #end if
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24 #if str( $rm_res ) != '' and str( $rm_res ) != 'None' :
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25 -rm_res "$rm_res"
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26 #end if
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27 | tail -n 5
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28 ]]></command>
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29 <inputs>
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30 <param name="i" label="input pdb-file" optional="false" type="data" format="pdb"/>
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31 <param name="lig_chain" label="chain-name of ligand" optional="false" area="true" type="text" size="1x15"/>
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32 <param name="lig_name" label="ligand name" optional="false" area="true" type="text" size="1x15"/>
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33 <param name="rm_ch" label="protein chains that are to be deleted" optional="true" area="true" type="text" size="1x15"/>
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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"/>
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35 </inputs>
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36 <outputs>
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37 <data name="rec" format="pdb"/>
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38 <data name="lig" format="pdb"/>
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39 </outputs>
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40 <help>This tool splits a given pdb-file into two files containing receptor and reference ligand, respectively.
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41
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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'.
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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'.
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44
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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>
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46 </tool>