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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [ForceFields]-->
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4 <tool id="CalculateEnergy" name="CalculateEnergy" version="1.1.0">
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5 <description>calculate free energy of a protein </description>
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6 <macros>
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7 <token name="@EXECUTABLE@">CalculateEnergy</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="stdio"/>
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11 <expand macro="requirements"/>
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12 <command>CalculateEnergy
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13
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14 #if $param_pdb:
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15 -pdb $param_pdb
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16 #end if
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17 #if $param_force_field:
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18 -force_field
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19 #if " " in str($param_force_field):
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20 "$param_force_field"
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21 #else
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22 $param_force_field
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23 #end if
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24 #end if
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25 #if $param_non_bond_cutoff:
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26 -non_bond_cutoff $param_non_bond_cutoff
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27 #end if
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28 #if $param_elec_stat_cuton:
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29 -elec_stat_cuton $param_elec_stat_cuton
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30 #end if
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31 #if $param_elec_stat_cutoff:
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32 -elec_stat_cutoff $param_elec_stat_cutoff
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33 #end if
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34 #if $param_dist_dep_dielec:
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35 -dist_dep_dielec $param_dist_dep_dielec
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36 #end if
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37 #if $param_overwrite_types:
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38 -overwrite_types $param_overwrite_types
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39 #end if
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40 #if $param_overwrite_charges:
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41 -overwrite_charges $param_overwrite_charges
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42 #end if
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43 </command>
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44 <inputs>
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45 <param name="param_pdb" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input pdb file" help="(-pdb) "/>
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46 <param name="param_force_field" type="select" optional="True" value="AMBER" label="force field (AMBER, MMFF94)" help="(-force_field) ">
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47 <option value="AMBER">AMBER</option>
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48 <option value=" MMFF94"> MMFF94</option>
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49 </param>
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50 <param name="param_non_bond_cutoff" type="float" value="20.0" label="cutoff radius in calculations of nonbonded interactions" help="(-non_bond_cutoff) "/>
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51 <param name="param_elec_stat_cuton" type="float" value="13.0" label="electrostatic cuton" help="(-elec_stat_cuton) "/>
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52 <param name="param_elec_stat_cutoff" type="float" value="15.0" label="electrostatic cutoff" help="(-elec_stat_cutoff) "/>
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53 <param name="param_dist_dep_dielec" type="integer" min="0" max="1" optional="True" value="0" label="apply distance dependent dielectric constant" help="(-dist_dep_dielec) "/>
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54 <param name="param_overwrite_types" type="integer" min="0" max="1" optional="True" value="0" label="overwrite even non-empty type names" help="(-overwrite_types) "/>
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55 <param name="param_overwrite_charges" type="integer" min="0" max="1" optional="True" value="0" label="overwrite even non-zero charges" help="(-overwrite_charges) "/>
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56 </inputs>
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57 <expand macro="advanced_options"/>
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58 <outputs>
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59 <data name="param_stdout" format="text" label="Output from stdout"/>
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60 </outputs>
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61 <help>This tool computes the free energy of a pdb file using a specified force field (-force_field) and force field parameters (-non_bond_cutoff, -elec_stat_cuton ... ).
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62
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63 </help>
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64 </tool>
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