Mercurial > repos > bimib > marea
comparison Desktop/Marea/marea_cluster.xml @ 30:e88efefbd015 draft
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author | bimib |
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date | Tue, 15 Oct 2019 12:21:16 -0400 |
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29:9fcb0e8d6d47 | 30:e88efefbd015 |
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1 <tool id="MaREA_cluester" name="Cluster Analysis" version="1.0.6"> | |
2 <description></description> | |
3 <macros> | |
4 <import>marea_macros.xml</import> | |
5 </macros> | |
6 <requirements> | |
7 <requirement type="package" version="0.25.1">pandas</requirement> | |
8 <requirement type="package" version="1.1.0">scipy</requirement> | |
9 <requirement type="package" version="0.10.1">cobra</requirement> | |
10 <requirement type="package" version="0.21.3">scikit-learn</requirement> | |
11 <requirement type="package" version="2.2.2">matplotlib</requirement> | |
12 <requirement type="package" version="1.17">numpy</requirement> | |
13 </requirements> | |
14 <command detect_errors="exit_code"> | |
15 <![CDATA[ | |
16 python $__tool_directory__/marea_cluster.py | |
17 --input $input | |
18 --tool_dir $__tool_directory__ | |
19 --out_log $log | |
20 --best_cluster $best_cluster | |
21 --cluster_type ${data.clust_type} | |
22 #if $data.clust_type == 'kmeans': | |
23 --k_min ${data.k_min} | |
24 --k_max ${data.k_max} | |
25 --elbow ${data.elbow} | |
26 --silhouette ${data.silhouette} | |
27 #end if | |
28 #if $data.clust_type == 'dbscan': | |
29 #if $data.dbscan_advanced.advanced == 'true' | |
30 --eps ${data.dbscan_advanced.eps} | |
31 --min_samples ${data.dbscan_advanced.min_samples} | |
32 #end if | |
33 #end if | |
34 #if $data.clust_type == 'hierarchy': | |
35 --k_min ${data.k_min} | |
36 --k_max ${data.k_max} | |
37 #end if | |
38 ]]> | |
39 </command> | |
40 <inputs> | |
41 <param name="input" argument="--input" type="data" format="tabular, csv, tsv" label="Input dataset" /> | |
42 | |
43 <conditional name="data"> | |
44 <param name="clust_type" argument="--cluster_type" type="select" label="Choose clustering type:"> | |
45 <option value="kmeans" selected="true">KMeans</option> | |
46 <option value="dbscan">DBSCAN</option> | |
47 <option value="hierarchy">Agglomerative Hierarchical</option> | |
48 </param> | |
49 <when value="kmeans"> | |
50 <param name="k_min" argument="--k_min" type="integer" min="2" max="20" value="2" label="Min number of clusters (k) to be tested" /> | |
51 <param name="k_max" argument="--k_max" type="integer" min="2" max="20" value="3" label="Max number of clusters (k) to be tested" /> | |
52 <param name="elbow" argument="--elbow" type="boolean" value="true" label="Draw the elbow plot from k-min to k-max"/> | |
53 <param name="silhouette" argument="--silhouette" type="boolean" value="true" label="Draw the Silhouette plot from k-min to k-max"/> | |
54 </when> | |
55 <when value="dbscan"> | |
56 <conditional name="dbscan_advanced"> | |
57 <param name="advanced" type="boolean" value="false" label="Want to use custom params for DBSCAN? (if not optimal values will be used)"> | |
58 <option value="true">Yes</option> | |
59 <option value="false">No</option> | |
60 </param> | |
61 <when value="false"></when> | |
62 <when value="true"> | |
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" /> | |
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)"/> | |
65 | |
66 </when> | |
67 </conditional> | |
68 </when> | |
69 <when value="hierarchy"> | |
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" /> | |
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" /> | |
72 </when> | |
73 </conditional> | |
74 </inputs> | |
75 | |
76 <outputs> | |
77 <data format="txt" name="log" label="${tool.name} - Log" /> | |
78 <data format="tabular" name="best_cluster" label="${tool.name} - Best cluster" /> | |
79 <collection name="results" type="list" label="${tool.name} - Plots and results"> | |
80 <discover_datasets pattern="__name_and_ext__" directory="clustering"/> | |
81 </collection> | |
82 </outputs> | |
83 <help> | |
84 <![CDATA[ | |
85 | |
86 What it does | |
87 ------------- | |
88 | |
89 | |
90 ]]> | |
91 </help> | |
92 <expand macro="citations" /> | |
93 </tool> | |
94 | |
95 |