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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="ExtractClustersFromWardTree" name="ExtractClustersFromWardTree" version="1.1.0">
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5 <description>extracts docking clusters </description>
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6 <macros>
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7 <token name="@EXECUTABLE@">ExtractClustersFromWardTree</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>ExtractClustersFromWardTree
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13
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14 #if $param_i:
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15 -i $param_i
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16 #end if
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17 #if $param_i_type:
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18 -i_type "$param_i_type"
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19 #end if
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20 #if $param_o_out:
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21 -o_out $param_o_out
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22 #end if
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23 #if $param_o_type:
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24 -o_type
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25 #if " " in str($param_o_type):
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26 "$param_o_type"
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27 #else
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28 $param_o_type
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29 #end if
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30 #end if
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31 #if $param_cutoff_type:
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32 -cutoff_type
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33 #if " " in str($param_cutoff_type):
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34 "$param_cutoff_type"
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35 #else
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36 $param_cutoff_type
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37 #end if
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38 #end if
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39 #if $param_cut_value:
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40 -cut_value $param_cut_value
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41 #end if
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42 #if $param_min_size:
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43 -min_size $param_min_size
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44 #end if
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45 </command>
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46 <inputs>
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47 <param name="param_i" type="data" format="dat" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input serialized cluster file" help="(-i) "/>
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48 <param name="param_i_type" type="text" size="30" value="binary" label="input type (binary, text)" help="(-i_type) ">
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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 <param name="param_o_type" type="select" optional="True" value="index_list" label="output type (gv, json, index_list)" help="(-o_type) ">
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57 <option value="gv">gv</option>
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58 <option value=" json"> json</option>
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59 <option value=" index_list"> index_list</option>
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60 </param>
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61 <param name="param_cutoff_type" type="select" optional="True" value="ward_distance" label="cutoff type (ward_distance, num_clusters)" help="(-cutoff_type) ">
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62 <option value="ward_distance">ward_distance</option>
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63 <option value=" num_clusters"> num_clusters</option>
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64 </param>
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65 <param name="param_cut_value" type="float" min="0.0" max="10000.0" optional="True" value="5.0" label="cut value for splitting the given WART tree using the cutoff-type (default 5.0)" help="(-cut_value) "/>
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66 <param name="param_min_size" type="integer" min="1" max="10000" optional="True" value="1" label="minimal size of clusters (default 1)" help="(-min_size) "/>
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67 </inputs>
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68 <expand macro="advanced_options"/>
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69 <outputs>
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70 <data name="param_o_out" format="gv"/>
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71 </outputs>
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72 <help>This tool extracts clusters of docking poses given a dat file.
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73
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74 Parameters are the filename (-i) of the serialized cluster tree, the output filename (-o_out), the output type (-o_type). The optional parameter -i_type allows to switch between binary (default) and text file for the cluster tree input, parameter -min_size allows to filter for cluster of a minimal size, parameter -cutoff_type defines the way to cut the cluster tree (either by ward distance or by a target number of clusters) using paramter -cut_value.
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75
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76 Output of this tool is the extracted cluster tree, either as index list, as graph visualization (gv) input, or as json
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77
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78 </help>
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79 </tool>
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