annotate Marea/marea_cluster.xml @ 33:abf0bfe01c78 draft

Uploaded
author bimib
date Wed, 16 Oct 2019 16:25:56 -0400
parents 944e15aa970a
children 1a97d1537623
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
33
abf0bfe01c78 Uploaded
bimib
parents: 31
diff changeset
1 <tool id="MaREA_cluester" name="Cluster Analysis" version="1.0.7">
29
9fcb0e8d6d47 Uploaded
bimib
parents: 28
diff changeset
2 <description></description>
16
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
3 <macros>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
4 <import>marea_macros.xml</import>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
5 </macros>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
6 <requirements>
17
640f303d0cec fix for dependencies
bimib
parents: 16
diff changeset
7 <requirement type="package" version="0.25.1">pandas</requirement>
16
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
8 <requirement type="package" version="1.1.0">scipy</requirement>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
9 <requirement type="package" version="0.10.1">cobra</requirement>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
10 <requirement type="package" version="0.21.3">scikit-learn</requirement>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
11 <requirement type="package" version="2.2.2">matplotlib</requirement>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
12 <requirement type="package" version="1.17">numpy</requirement>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
13 </requirements>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
14 <command detect_errors="exit_code">
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
15 <![CDATA[
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
16 python $__tool_directory__/marea_cluster.py
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
17 --input $input
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
18 --tool_dir $__tool_directory__
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
19 --out_log $log
28
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 27
diff changeset
20 --best_cluster $best_cluster
24
69ed2562e81e Uploaded
bimib
parents: 18
diff changeset
21 --cluster_type ${data.clust_type}
16
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
22 #if $data.clust_type == 'kmeans':
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
23 --k_min ${data.k_min}
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
24 --k_max ${data.k_max}
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
25 --elbow ${data.elbow}
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
26 --silhouette ${data.silhouette}
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
27 #end if
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
28 #if $data.clust_type == 'dbscan':
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
29 #if $data.dbscan_advanced.advanced == 'true'
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
30 --eps ${data.dbscan_advanced.eps}
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
31 --min_samples ${data.dbscan_advanced.min_samples}
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
32 #end if
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
33 #end if
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
34 #if $data.clust_type == 'hierarchy':
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
35 --k_min ${data.k_min}
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
36 --k_max ${data.k_max}
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
37 #end if
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
38 ]]>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
39 </command>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
40 <inputs>
31
944e15aa970a Uploaded
bimib
parents: 29
diff changeset
41 <param name="input" argument="--input" type="data" format="tabular, csv, tsv" label="Input dataset" />
16
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
42
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
43 <conditional name="data">
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
44 <param name="clust_type" argument="--cluster_type" type="select" label="Choose clustering type:">
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
45 <option value="kmeans" selected="true">KMeans</option>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
46 <option value="dbscan">DBSCAN</option>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
47 <option value="hierarchy">Agglomerative Hierarchical</option>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
48 </param>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
49 <when value="kmeans">
31
944e15aa970a Uploaded
bimib
parents: 29
diff changeset
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" />
944e15aa970a Uploaded
bimib
parents: 29
diff changeset
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" />
16
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
52 <param name="elbow" argument="--elbow" type="boolean" value="true" label="Draw the elbow plot from k-min to k-max"/>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
53 <param name="silhouette" argument="--silhouette" type="boolean" value="true" label="Draw the Silhouette plot from k-min to k-max"/>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
54 </when>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
55 <when value="dbscan">
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
56 <conditional name="dbscan_advanced">
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
57 <param name="advanced" type="boolean" value="false" label="Want to use custom params for DBSCAN? (if not optimal values will be used)">
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
58 <option value="true">Yes</option>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
59 <option value="false">No</option>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
60 </param>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
61 <when value="false"></when>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
62 <when value="true">
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
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" />
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
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)"/>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
65
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
66 </when>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
67 </conditional>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
68 </when>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
69 <when value="hierarchy">
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
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" />
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
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" />
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
72 </when>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
73 </conditional>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
74 </inputs>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
75
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
76 <outputs>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
77 <data format="txt" name="log" label="${tool.name} - Log" />
33
abf0bfe01c78 Uploaded
bimib
parents: 31
diff changeset
78 <data format="tabular" name="best_cluster" label="${tool.name} - best cluster assignment" />
28
e6831924df01 small fixes (elbow plot and output managment)
bimib
parents: 27
diff changeset
79 <collection name="results" type="list" label="${tool.name} - Plots and results">
16
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
80 <discover_datasets pattern="__name_and_ext__" directory="clustering"/>
33
abf0bfe01c78 Uploaded
bimib
parents: 31
diff changeset
81 <filter>data['clust_type'] == "kmeans" or data['clust_type'] == "hierarchy"</filter>
16
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
82 </collection>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
83 </outputs>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
84 <help>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
85 <![CDATA[
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
86
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
87 What it does
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
88 -------------
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
89
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
90
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
91 ]]>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
92 </help>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
93 <expand macro="citations" />
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
94 </tool>
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
95
c71ac0bb12de Uploaded
bimib
parents: 8
diff changeset
96