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comparison Marea/marea_cluster.xml @ 31:944e15aa970a draft

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author bimib
date Tue, 15 Oct 2019 12:22:43 -0400
parents 9fcb0e8d6d47
children abf0bfe01c78
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30:e88efefbd015 31:944e15aa970a
1 <tool id="MaREA_cluester" name="Cluster Analysis" version="1.0.5"> 1 <tool id="MaREA_cluester" name="Cluster Analysis" version="1.0.6">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>marea_macros.xml</import> 4 <import>marea_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
36 --k_max ${data.k_max} 36 --k_max ${data.k_max}
37 #end if 37 #end if
38 ]]> 38 ]]>
39 </command> 39 </command>
40 <inputs> 40 <inputs>
41 <param name="input" argument="--input" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" /> 41 <param name="input" argument="--input" type="data" format="tabular, csv, tsv" label="Input dataset" />
42 42
43 <conditional name="data"> 43 <conditional name="data">
44 <param name="clust_type" argument="--cluster_type" type="select" label="Choose clustering type:"> 44 <param name="clust_type" argument="--cluster_type" type="select" label="Choose clustering type:">
45 <option value="kmeans" selected="true">KMeans</option> 45 <option value="kmeans" selected="true">KMeans</option>
46 <option value="dbscan">DBSCAN</option> 46 <option value="dbscan">DBSCAN</option>
47 <option value="hierarchy">Agglomerative Hierarchical</option> 47 <option value="hierarchy">Agglomerative Hierarchical</option>
48 </param> 48 </param>
49 <when value="kmeans"> 49 <when value="kmeans">
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" /> 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="3" max="99" value="5" label="Max 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"/> 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"/> 53 <param name="silhouette" argument="--silhouette" type="boolean" value="true" label="Draw the Silhouette plot from k-min to k-max"/>
54 </when> 54 </when>
55 <when value="dbscan"> 55 <when value="dbscan">
56 <conditional name="dbscan_advanced"> 56 <conditional name="dbscan_advanced">