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1 <tool id="MaREA_cluester" name="Cluster Analysis" version="1.0.4">
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2 <description>of Reaction Activity Scores</description>
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3 <macros>
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4 <import>marea_macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="0.25.1">pandas</requirement>
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8 <requirement type="package" version="1.1.0">scipy</requirement>
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9 <requirement type="package" version="0.10.1">cobra</requirement>
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10 <requirement type="package" version="0.21.3">scikit-learn</requirement>
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11 <requirement type="package" version="2.2.2">matplotlib</requirement>
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12 <requirement type="package" version="1.17">numpy</requirement>
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13 </requirements>
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14 <command detect_errors="exit_code">
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15 <![CDATA[
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16 python $__tool_directory__/marea_cluster.py
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17 --input $input
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18 --tool_dir $__tool_directory__
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19 --out_log $log
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20 --best_cluster $best_cluster
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21 --cluster_type ${data.clust_type}
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22 #if $data.clust_type == 'kmeans':
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23 --k_min ${data.k_min}
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24 --k_max ${data.k_max}
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25 --elbow ${data.elbow}
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26 --silhouette ${data.silhouette}
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27 #end if
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28 #if $data.clust_type == 'dbscan':
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29 #if $data.dbscan_advanced.advanced == 'true'
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30 --eps ${data.dbscan_advanced.eps}
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31 --min_samples ${data.dbscan_advanced.min_samples}
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32 #end if
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33 #end if
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34 #if $data.clust_type == 'hierarchy':
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35 --k_min ${data.k_min}
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36 --k_max ${data.k_max}
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37 #end if
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38 ]]>
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39 </command>
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40 <inputs>
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41 <param name="input" argument="--input" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />
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42
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43 <conditional name="data">
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44 <param name="clust_type" argument="--cluster_type" type="select" label="Choose clustering type:">
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45 <option value="kmeans" selected="true">KMeans</option>
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46 <option value="dbscan">DBSCAN</option>
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47 <option value="hierarchy">Agglomerative Hierarchical</option>
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48 </param>
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49 <when value="kmeans">
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50 <param name="k_min" argument="--k_min" type="integer" min="1" max="99" value="3" label="Min number of clusters (k) to be tested" />
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51 <param name="k_max" argument="--k_max" type="integer" min="3" max="99" value="5" label="Max number of clusters (k) to be tested" />
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52 <param name="elbow" argument="--elbow" type="boolean" value="true" label="Draw the elbow plot from k-min to k-max"/>
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53 <param name="silhouette" argument="--silhouette" type="boolean" value="true" label="Draw the Silhouette plot from k-min to k-max"/>
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54 </when>
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55 <when value="dbscan">
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56 <conditional name="dbscan_advanced">
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57 <param name="advanced" type="boolean" value="false" label="Want to use custom params for DBSCAN? (if not optimal values will be used)">
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58 <option value="true">Yes</option>
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59 <option value="false">No</option>
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60 </param>
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61 <when value="false"></when>
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62 <when value="true">
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63 <param name="eps" argument="--eps" type="float" value="0.5" label="Epsilon - The maximum distance between two samples for one to be considered as in the neighborhood of the other" />
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64 <param name="min_samples" argument="min_samples" type="integer" value="5" label="Min samples - The number of samples in a neighborhood for a point to be considered as a core point (this includes the point itself)"/>
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65
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66 </when>
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67 </conditional>
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68 </when>
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69 <when value="hierarchy">
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70 <param name="k_min" argument="--k_min" type="integer" min="2" max="99" value="3" label="Min number of clusters (k) to be tested" />
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71 <param name="k_max" argument="--k_max" type="integer" min="3" max="99" value="5" label="Max number of clusters (k) to be tested" />
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72 </when>
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73 </conditional>
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74 </inputs>
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75
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76 <outputs>
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77 <data format="txt" name="log" label="${tool.name} - Log" />
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78 <data format="tabular" name="best_cluster" label="${tool.name} - Best cluster" />
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79 <collection name="results" type="list" label="${tool.name} - Plots and results">
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80 <discover_datasets pattern="__name_and_ext__" directory="clustering"/>
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81 </collection>
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82 </outputs>
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83 <help>
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84 <![CDATA[
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85
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86 What it does
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87 -------------
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88
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89
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90 ]]>
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91 </help>
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92 <expand macro="citations" />
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93 </tool>
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94
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95
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