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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: [Docking]-->
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4 <tool id="PDBRMSDCalculator" name="PDBRMSDCalculator" version="1.1.0">
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5 <description>computes RMSD between protein poses </description>
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6 <macros>
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7 <token name="@EXECUTABLE@">PDBRMSDCalculator</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>PDBRMSDCalculator
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13
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14 #if $param_i_pdb:
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15 -i_pdb $param_i_pdb
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16 #end if
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17 #if $param_i_query:
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18 -i_query $param_i_query
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19 #end if
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20 #if $param_i_type:
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21 -i_type
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22 #if " " in str($param_i_type):
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23 "$param_i_type"
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24 #else
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25 $param_i_type
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26 #end if
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27 #end if
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28 #if $param_o:
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29 -o $param_o
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30 #end if
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31 #if $param_scope:
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32 -scope
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33 #if " " in str($param_scope):
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34 "$param_scope"
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35 #else
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36 $param_scope
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37 #end if
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38 #end if
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39 #if $param_rmsd_type:
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40 -rmsd_type
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41 #if " " in str($param_rmsd_type):
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42 "$param_rmsd_type"
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43 #else
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44 $param_rmsd_type
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45 #end if
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46 #end if
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47 </command>
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48 <inputs>
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49 <param name="param_i_pdb" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input pdb-file" help="(-i_pdb) "/>
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50 <param name="param_i_query" type="data" format="dcd,txt,pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="molecule(s) to compare input file" help="(-i_query) "/>
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51 <param name="param_i_type" type="select" optional="True" value="pdb" label="query type (pdb, dcd, or transformation file (rigid_transformations)" help="(-i_type) ">
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52 <option value="pdb">pdb</option>
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53 <option value=" dcd"> dcd</option>
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54 <option value=" rigid_transformations"> rigid_transformations</option>
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55 </param>
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56 <param name="param_scope" type="select" optional="True" value="C_ALPHA" label="atoms to be considered for scoreing a pose (C_ALPHA, BACKBONE, ALL_ATOMS)" help="(-scope) ">
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57 <option value="C_ALPHA">C_ALPHA</option>
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58 <option value=" BACKBONE"> BACKBONE</option>
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59 <option value=" ALL_ATOMS"> ALL_ATOMS</option>
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60 </param>
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61 <param name="param_rmsd_type" type="select" optional="True" value="SNAPSHOT_RMSD" label="rmsd type used for clustering (SNAPSHOT_RMSD, RIGID_RMSD, CENTER_OF_MASS_DISTANCE)" help="(-rmsd_type) ">
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62 <option value="SNAPSHOT_RMSD">SNAPSHOT_RMSD</option>
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63 <option value=" RIGID_RMSD"> RIGID_RMSD</option>
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64 <option value=" CENTER_OF_MASS_DISTANCE"> CENTER_OF_MASS_DISTANCE</option>
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65 </param>
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66 </inputs>
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67 <expand macro="advanced_options"/>
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68 <outputs>
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69 <data name="param_o" format="txt"/>
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70 </outputs>
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71 <help>This tool computes the RMSD between proteins.
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72
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73 Parameters are either a second input file (i_query) who's type has to be specified (i_type) and can be either a single pdb, a dcd or a transformation file. Optional parameters are the rmsd type (-rmsd_type), and the type of atoms used for scoring a pose (-scope).
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74
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75 Output of this tool is a either the rmsd (in the pdb-pdb case) or a file (-o) containing the RMSD between the first pose and all other poses.
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76
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77 </help>
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78 </tool>
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