Mercurial > repos > iuc > deepmicro
annotate deepmicro.xml @ 0:77cbfe3e1b0d draft
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
author | iuc |
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date | Tue, 02 May 2023 17:39:13 +0000 |
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children | c58c1a99578b |
rev | line source |
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0
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
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1 <tool id="deepmicro" name="DeepMicro" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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2 <description> |
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planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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3 Representation learning and classification framework |
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planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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4 </description> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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5 <macros> |
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planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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6 <import>macros.xml</import> |
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planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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7 </macros> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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8 <expand macro="biotools" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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9 <expand macro="requirements" /> |
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planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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10 <expand macro="version" /> |
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planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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11 <command detect_errors="exit_code"><![CDATA[ |
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planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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12 mkdir data && |
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planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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13 mkdir results && |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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14 ln -s '$features' data/features.csv && |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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15 |
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planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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16 #if $mode.mode_type == "only_encoding": |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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17 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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18 #for $params in $mode.parameter_set: |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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19 |
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planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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20 #if $params.rl_type.rl_type_choice == "--pca" or $params.rl_type.rl_type_choice == "--rp": |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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21 DM.py -r 1 -cd features.csv '$params.rl_type.rl_type_choice' --save_rep --no_clf -t \${GALAXY_SLOTS:-8} && |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
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22 #else: |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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23 DM.py -r 1 -cd features.csv '$params.rl_type.rl_type_choice' -dm '$params.rl_type.dm' --save_rep --no_clf -t \${GALAXY_SLOTS:-8} && |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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24 #end if |
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planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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25 #end for |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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26 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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27 #else: |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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28 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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29 ln -s '$mode.class_labels' data/labels.csv && |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
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30 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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31 #for $params in $mode.parameter_set: |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
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32 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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33 #if $params.rl_type.rl_type_choice == "--pca" or $params.rl_type.rl_type_choice == "--rp": |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
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34 DM.py -r 1 -cd features.csv -cl labels.csv '$params.rl_type.rl_type_choice' --save_rep -m '$params.rl_type.classifier' -t \${GALAXY_SLOTS:-8} && |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
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35 #else: |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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36 DM.py -r 1 -cd features.csv -cl labels.csv '$params.rl_type.rl_type_choice' -dm '$params.rl_type.dm' --save_rep -m '$params.rl_type.classifier' -t \${GALAXY_SLOTS:-8} && |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
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37 #end if |
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planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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38 #end for |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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39 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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40 #end if |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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41 |
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planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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42 echo Done ! |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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43 ]]> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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44 </command> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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45 <inputs> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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46 <param argument="--features" type="data" format="tabular" label="Feature table" help="Dataset containing the features of samples"/> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
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47 <conditional name="mode"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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48 <param name="mode_type" type="select" label="Mode" help="The tool can either only create a latent |
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planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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49 representation of the data or create a latent representation of the data and cross validate a classifier using that encoding."> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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50 <option value="only_encoding">Create only encoding</option> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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51 <option value="e_and_c">Create encoding and cross validate a classifier</option> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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52 </param> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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53 <when value="only_encoding"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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54 <repeat name="parameter_set" title="Parameter Set"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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55 <conditional name="rl_type"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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56 <param name="rl_type_choice" type="select" label="Representation learning type" help="The type of representation learning" > |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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57 <option value="--pca">PCA</option> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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58 <option value="--rp">Random Projection</option> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
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59 <option value="--ae">Autoencoder or Deep Autoencoder</option> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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60 <option value="--vae">Variational Autoencoder</option> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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61 <option value="--cae">Convolutional Autoencoder</option> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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62 </param> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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63 <when value="--pca"/> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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64 <when value="--rp"/> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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65 <when value="--ae"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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66 <expand macro="dm" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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67 </when> |
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planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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68 <when value="--vae"> |
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planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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69 <expand macro="dm" /> |
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70 </when> |
77cbfe3e1b0d
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71 <when value="--cae"> |
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planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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72 <expand macro="dm" /> |
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73 </when> |
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74 </conditional> |
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75 </repeat> |
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76 </when> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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77 <when value="e_and_c"> |
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planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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78 <param argument="--class_labels" type="data" format="tabular" label="Class labels" help="Dataset containing the class labels corresponding to the features"/> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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79 <repeat name="parameter_set" title="Parameter Set"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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80 <conditional name="rl_type"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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81 <param name="rl_type_choice" type="select" label="Representation learning type" help="The type of representation learning. `Train on input` trains the classifier on the input features without representation learning" > |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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82 <option value="--pca">PCA</option> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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83 <option value="--rp">Random Projection</option> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
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84 <option value="--ae">Autoencoder or Deep Autoencoder</option> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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85 <option value="--vae">Variational Autoencoder</option> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
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86 <option value="--cae">Convolutional Autoencoder</option> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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87 <option value="no_rl">Train on input</option> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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88 </param> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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89 <when value="no_rl"> |
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planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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90 <expand macro="clfs" /> |
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91 </when> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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92 <when value="--pca"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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93 <expand macro="clfs" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
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94 </when> |
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95 <when value="--rp"> |
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96 <expand macro="clfs" /> |
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97 </when> |
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98 <when value="--ae"> |
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99 <expand macro="dm" /> |
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100 <expand macro="clfs" /> |
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101 </when> |
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102 <when value="--vae"> |
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103 <expand macro="dm" /> |
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104 <expand macro="clfs" /> |
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105 </when> |
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106 <when value="--cae"> |
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107 <expand macro="dm" /> |
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108 <expand macro="clfs" /> |
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109 </when> |
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110 </conditional> |
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111 </repeat> |
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112 </when> |
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113 </conditional> |
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114 </inputs> |
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115 <outputs> |
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116 <data name="results" format="tabular" from_work_dir="./results/*_result.txt" label="${tool.name} on ${on_string}: Results"> |
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117 <!-- results are only for classifiers --> |
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118 <filter>mode["mode_type"] == "e_and_c"</filter> |
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119 </data> |
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120 <collection name="encoded_features" type="list" label="Encoded Features"> |
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121 <!-- the encoded features generated by the tool are only for the training set, this is not very useful, therefore omitting |
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122 todo change tool do export features complete dataset also when classification is performed --> |
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123 <filter>mode["mode_type"] == "only_encoding"</filter> |
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124 <discover_datasets directory="results" pattern="(?P<designation>.*)_rep\.csv" format="tabular" visible="false" /> |
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125 </collection> |
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126 </outputs> |
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127 <tests> |
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128 |
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129 <!-- only encoding --> |
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130 <!-- test one parameter sets --> |
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131 |
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132 <test expect_num_outputs="1"> |
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133 <param name="mode_type" value="only_encoding" /> |
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134 <param name="features" value="UserDataExample.csv" /> |
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135 <param name="rl_type_choice" value="--ae" /> |
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136 <param name="dm" value="40" /> |
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137 <output_collection name="encoded_features" type="list"> |
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138 <!-- output is non determinisitc --> |
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139 <element name="AE[40]_features" ftype="tabular" > |
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140 <assert_contents> |
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141 <has_n_lines n="20"/> |
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142 <!-- <has_n_columns n="40" sep="," /> --> |
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143 </assert_contents> |
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144 </element> |
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145 </output_collection> |
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146 </test> |
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147 |
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148 <test expect_num_outputs="1"> |
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149 <param name="mode_type" value="only_encoding" /> |
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150 <param name="features" value="UserDataExample.csv" /> |
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151 <param name="rl_type_choice" value="--pca" /> |
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152 <output_collection name="encoded_features" type="list"> |
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153 <element name="PCA_features" ftype="tabular" > |
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154 <assert_contents> |
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155 <has_n_lines n="20"/> |
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156 <!-- <has_n_columns n="40" sep="," /> --> |
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157 </assert_contents> |
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158 </element> |
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159 </output_collection> |
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160 </test> |
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161 |
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162 <!-- test multiple parameter sets --> |
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163 <test expect_num_outputs="1"> |
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164 <param name="features" value="UserDataExample.csv" /> |
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165 <conditional name="mode"> |
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166 <param name="mode_type" value="only_encoding" /> |
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167 |
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168 <repeat name="parameter_set"> |
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169 <conditional name="rl_type"> |
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170 <param name="rl_type_choice" value="--pca" /> |
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171 </conditional> |
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172 </repeat> |
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173 |
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174 <repeat name="parameter_set"> |
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175 <conditional name="rl_type"> |
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176 <param name="rl_type_choice" value="--ae" /> |
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177 <param name="dm" value="40" /> |
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178 </conditional> |
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179 </repeat> |
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180 |
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181 </conditional> |
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182 |
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183 <output_collection name="encoded_features" type="list"> |
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184 <element name="AE[40]_features" ftype="tabular" > |
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185 <assert_contents> |
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186 <has_n_lines n="20"/> |
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187 <!-- <has_n_columns n="40" sep="," /> --> |
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188 </assert_contents> |
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189 </element> |
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190 <element name="PCA_features" ftype="tabular" > |
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191 <assert_contents> |
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192 <has_n_lines n="20"/> |
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193 <!-- <has_n_columns n="40" sep="," /> --> |
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194 </assert_contents> |
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195 </element> |
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196 </output_collection> |
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197 |
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198 </test> |
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199 |
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200 <!-- encoding and clf --> |
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201 <!-- test one parameter set --> |
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202 |
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203 <test expect_num_outputs="1"> |
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204 <param name="features" value="UserDataExample.csv" /> |
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205 <param name="mode_type" value="e_and_c" /> |
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206 <param name="class_labels" value="UserLabelExample.csv" /> |
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207 <param name="rl_type_choice" value="--vae" /> |
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208 <param name="dm" value="40" /> |
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209 <param name="classifier" value="rf" /> |
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210 <output ftype="tabular" name="results" > |
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211 <assert_contents> |
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212 <has_text text="VAE[40]_rf" /> |
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213 </assert_contents> |
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214 </output> |
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215 |
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216 </test> |
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217 |
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218 <!-- test multiple parameter sets --> |
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219 <test expect_num_outputs="1"> |
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220 <param name="features" value="UserDataExample.csv" /> |
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221 <conditional name="mode"> |
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222 <param name="mode_type" value="e_and_c" /> |
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223 <param name="class_labels" value="UserLabelExample.csv" /> |
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224 |
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225 <repeat name="parameter_set"> |
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226 <conditional name="rl_type"> |
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227 <param name="rl_type_choice" value="--cae" /> |
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228 <param name="dm" value="20" /> |
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229 <param name="classifier" value="rf" /> |
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230 </conditional> |
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231 </repeat> |
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232 |
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233 <repeat name="parameter_set"> |
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234 <conditional name="rl_type"> |
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235 <param name="rl_type_choice" value="--vae" /> |
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236 <param name="dm" value="40" /> |
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237 <param name="classifier" value="mlp" /> |
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238 </conditional> |
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239 </repeat> |
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240 |
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241 </conditional> |
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242 |
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243 <output ftype="tabular" name="results" > |
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244 <assert_contents> |
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245 <has_text text="CAE[20]_rf" /> |
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246 <has_text text="VAE[40]_mlp" /> |
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247 </assert_contents> |
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248 </output> |
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249 |
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250 </test> |
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251 |
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252 </tests> |
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253 <help> |
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254 <![CDATA[ |
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255 DeepMicro is a deep representation learning framework exploiting various autoencoders |
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256 to learn robust low-dimensional representations from high-dimensional data and training |
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257 classification models based on the learned representation. |
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258 |
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259 ====================================== |
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260 Option 1) Only representation learning |
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261 ====================================== |
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262 |
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263 The representation learning does not require class labels and can be learned from the features alone. |
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264 The wrapper allows to explore multiple paramertes (i.e. different modes to |
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265 generate the features, please refer to the publication for details), for each |
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266 added parameter the encoded features are generated. Those features can then be passed to subsequent ML tools, |
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267 such as `Ensemble methods for classification and regression` or `Split Dataset into training and test subsets` |
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268 |
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269 ===================================================== |
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270 Option 2) Representation learning and classification |
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271 ===================================================== |
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272 |
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273 The tool itself can also evaluate the performance of the generated representation learning for different |
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274 classifiers internally using 5 fold CV. The wrapper allows to explore multiple paramertes and clfs. |
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275 Each parameter run will be stored as a line to the result file. If this option is chosen the latent representation is not |
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276 exported as output. To create the latent representation of the complete feature set, run the tool again |
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277 with the same parameters using the `Only representation learning` option. |
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278 The header of the result file is: |
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279 |
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280 '{Encoding}_{classifier}, AUC, ACC, Recall, Precision, F1_score, time-end, runtime(sec), classfication time(sec), best hyper-parameter' |
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281 |
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282 The overall schema of the tool is shown in: |
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283 |
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284 .. image:: ML_Workflow.png |
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285 ]]> |
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286 </help> |
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287 <expand macro="citations" /> |
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288 <expand macro="creator" /> |
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289 </tool> |