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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: [Convert, combine and store]-->
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4 <tool id="PoseIndices2PDB" name="PoseIndices2PDB" version="1.1.0">
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5 <description>converts pose indices into PDB files </description>
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6 <macros>
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7 <token name="@EXECUTABLE@">PoseIndices2PDB</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>PoseIndices2PDB
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13
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14 #if $param_i_clust:
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15 -i_clust $param_i_clust
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16 #end if
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17 #if $param_i_trans:
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18 -i_trans $param_i_trans
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19 #end if
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20 #if $param_i_pdb:
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21 -i_pdb $param_i_pdb
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22 #end if
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23 #if $param_o:
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24 -o $param_o
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25 #end if
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26 #if $adv_opts.adv_opts_selector=='advanced':
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27 #if $adv_opts.param_o_id:
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28 -o_id "$adv_opts.param_o_id"
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29 #end if
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30 #if $adv_opts.param_o_dir:
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31 -o_dir "$adv_opts.param_o_dir"
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32 #end if
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33 #end if
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34 </command>
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35 <inputs>
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36 <param name="param_i_clust" type="data" format="txt" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input cluster index file" help="(-i_clust) "/>
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37 <param name="param_i_trans" type="data" format="dcd" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input tranformation file" help="(-i_trans) "/>
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38 <param name="param_i_pdb" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input reference pdb file" help="(-i_pdb) "/>
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39 <expand macro="advanced_options">
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40 <param name="param_o_id" type="text" size="30" value="$o.id" label="output file name prefix for 2nd to last pdb file" help="(-o_id) ">
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41 <sanitizer>
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42 <valid initial="string.printable">
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43 <remove value="'"/>
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44 <remove value="""/>
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45 </valid>
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46 </sanitizer>
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47 </param>
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48 <param name="param_o_dir" type="text" size="30" value="$__new_file_path__" label="output directory for 2nd to last pdb file" help="(-o_dir) ">
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49 <sanitizer>
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50 <valid initial="string.printable">
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51 <remove value="'"/>
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52 <remove value="""/>
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53 </valid>
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54 </sanitizer>
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55 </param>
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56 </expand>
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57 </inputs>
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58 <outputs>
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59 <data name="param_o" format="pdb"/>
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60 </outputs>
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61 <help>This tool converts all pose indices from a given transformation file and the corresponding reference PDBFile into separate PDBFiles.
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62
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63 Parameters are the input pose index file (-i_clust), the original transformation file (-i_trans), the corresponding reference pdb file (-i_pdb) and a naming schema for the resulting pdb files (-o).
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64
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65 Output of this tool is a set of PDBFiles representing the docking poses belonging to the given input cluster.
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66
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67 </help>
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68 </tool>
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