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1 <tool id="bg_eden_nearest_neighbor" name="EDeN Nearest Neighbors" version="0.1">
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2 <description></description>
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7
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3 <expand macro="requirements" />
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3
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4 <macros>
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5 <import>eden_macros.xml</import>
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6 </macros>
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7 <command>
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8 tmp_dir=`mktemp -d -u`;
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9 EDeN --action NEAREST_NEIGHBOR
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2
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10
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11 --input_data_file_name $infile
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12 --target_file_name $target_infile
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13
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14 --file_type "SPARSE_VECTOR"
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15 --binary_file_type
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16
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17 --output_directory_path \$tmp_dir
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18
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19
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20 ##
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21 ## shuffling files to create the correct outputs for Galaxy
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22 ##
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23
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24 ;
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25 cp \$tmp_dir/knn $ofile_nnlist 2> /dev/null
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26
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27 ## Nearest neighbor feature representation
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28 #if 'nnf' in str($additional_outputs).split(','):
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29 ;
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30 cp \$tmp_dir/knn_feature $ofile_nnf 2> /dev/null
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31 #end if
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32
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33 ## Nearest neighbor target value list
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34 #if 'nnt' in str($additional_outputs).split(','):
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35 ;
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36 cp \$tmp_dir/knn_target_value $ofile_nnt 2> /dev/null
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37 #end if
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38
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39 ## Nearest neighbor kernel value list
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40 #if 'nnk' in str($additional_outputs).split(','):
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41 ;
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42 cp \$tmp_dir/knn_kernel_value $ofile_nnk 2> /dev/null
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43 #end if
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44
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45 </command>
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46 <inputs>
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47
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48 <param format="eden_sparse_vector" name="infile" type="data" label="Input Graph" help=""/>
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49 <param format="txt" name="target_infile" type="data" label="Target file" help=""/>
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50
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2
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51 <expand macro="input_smooth_conditional" />
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52
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53 <expand macro="kernel_type_options" />
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54
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55 <expand macro="graph_types" />
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56
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57 <expand macro="normalization_kernel_hash_radius_dist_vertex" />
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58
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59 <param name="additional_outputs" type="select" multiple="true" optional="True" label="Additional outputs">
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60 <option value="none" selected="True">No additional output</option>
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61 <option value="nnk">Nearest neighbor kernel value list</option>
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62 <option value="nnt">Nearest neighbor target value list</option>
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63 <option value="nnf">Nearest neighbor feature representation</option>
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64 </param>
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65
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66 </inputs>
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67 <outputs>
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68 <data format="tabular" name="ofile_nnlist" label="${tool.name} on ${on_string}"/>
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69 <data format="tabular" name="ofile_nnf" label="${tool.name} on ${on_string} (Nearest neighbor feature representation)">
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70 <filter>'nnf' in additional_outputs</filter>
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71 </data>
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72 <data format="tabular" name="ofile_nnt" label="${tool.name} on ${on_string} (Nearest neighbor target value list)">
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73 <filter>'nnt' in additional_outputs</filter>
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74 </data>
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75 <data format="tabular" name="ofile_nnk" label="${tool.name} on ${on_string} (Nearest neighbor kernel value list)">
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76 <filter>'nnk' in additional_outputs</filter>
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77 </data>
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78 </outputs>
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79 <tests>
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80 <test>
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81 <param name="infile" value="3_molceuls.sdf" />
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82 <output name="outfile" file="3_molecules.gspan" />
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83 </test>
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84 </tests>
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85 <help>
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86
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87 .. class:: infomark
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88
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89 **What it does**
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90
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91 Nearest neighbors are efficiently identified with a locality sensitive hashing technique.
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92
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93 @references@
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94
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95 </help>
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96 </tool>
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