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1 <tool id="maximal_information_based_nonparametric_exploration" name="MINE" version="0.0.1">
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2 <description>- Maximal Information-based Nonparametric Exploration</description>
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3 <requirements>
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4 <requirement type="package" version="1.0.1">MINE</requirement>
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5 </requirements>
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6 <command interpreter="python">mine_wrapper.py
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7 --jar "\${JAVA_JAR_PATH}/MINE.jar"
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8
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9 --infile "${input_file}"
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10
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11 #if str( $master_variable_type.master_variable_type_selector ) in [ 'allPairs', 'adjacentPairs' ]:
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12 --master_variable "${master_variable_type.master_variable_type_selector}"
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13 #else:
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14 --master_variable "${master_variable_type.master_variable}"
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15 #end if
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16
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17 --cv "${cv}"
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18
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19 --exp "${exp}"
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20
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21 --c "${c}"
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22
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23 ##--gc ##skip
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24
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25
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26 #if str( $master_variable_type.master_variable_type_selector ) != 'allPairs' and $master_variable_type.permute:
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27 --permute
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28 #end if
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29
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30 --output_results "${output_results}"
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31
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32 --output_log "${output_log}"
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33 </command>
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34 <inputs>
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35 <param name="input_file" type="data" format="csv" label="CSV file" />
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36
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37 <conditional name="master_variable_type">
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38 <param name="master_variable_type_selector" type="select" label="Choose the master variable type">
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39 <option value="allPairs">allPairs</option>
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40 <option value="adjacentPairs">adjacentPairs</option>
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41 <option value="compare_against_ith" selected="True">compare against i-th</option>
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42 </param>
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43 <when value="compare_against_ith">
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44 <param type="integer" value="0" name="master_variable" />
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45 <param type="boolean" truevalue="--permute" false_value="" name="permute" checked="False" />
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46 </when>
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47 <when value="adjacentPairs">
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48 <param type="boolean" truevalue="--permute" false_value="" name="permute" checked="False" />
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49 </when>
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50 </conditional>
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51
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52 <param type="float" value="0" name="cv" />
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53
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54 <param type="float" value="0.6" name="exp" />
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55
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56 <param type="float" value="15" name="c" />
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57
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58 </inputs>
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59 <outputs>
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60 <data format="csv" name="output_results" label="${tool.name} on ${on_string} (Results)" />
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61 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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62 </outputs>
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63 <tests>
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64 <!-- TODO -->
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65 </tests>
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66 <help>
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67 **What it does**
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68
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69 Applies the Maximal Information-based Nonparametric Exploration strategy to an input dataset.
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70
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71 See http://www.exploredata.net/ for more information.
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72
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73 ------
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74
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75 **Citation**
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76
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77 For the underlying tool, please cite `David N. Reshef, Yakir A. Reshef, Hilary K. Finucane5, Sharon R. Grossman, Gilean McVean, Peter J. Turnbaugh, Eric S. Lander, Michael Mitzenmacher, Pardis C. Sabeti Detecting Novel Associations in Large Data Sets. Science. 2011 Dec. <http://www.sciencemag.org/content/334/6062/1518>`_
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78
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79 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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80
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81 </help>
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82 </tool>
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