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

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30:e88efefbd015

<tool id="MaREA_cluester" name="Cluster Analysis" version="1.0.5">
    <description></description>
    <macros>
        <import>marea_macros.xml</import>
    </macros>
    <requirements>

        	--k_max ${data.k_max}
      	#end if
        ]]>
    </command>
    <inputs>
        <param name="input" argument="--input" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />
        
        <conditional name="data">
			<param name="clust_type" argument="--cluster_type" type="select" label="Choose clustering type:">
                	<option value="kmeans" selected="true">KMeans</option>
                	<option value="dbscan">DBSCAN</option>
                	<option value="hierarchy">Agglomerative Hierarchical</option>
        	</param>
        	<when value="kmeans">
        		<param name="k_min" argument="--k_min" type="integer" min="1" max="99" value="3" label="Min number of clusters (k) to be tested" />
        		<param name="k_max" argument="--k_max" type="integer" min="3" max="99" value="5" label="Max number of clusters (k) to be tested" />
        		<param name="elbow" argument="--elbow" type="boolean" value="true" label="Draw the elbow plot from k-min to k-max"/>
        		<param name="silhouette" argument="--silhouette" type="boolean" value="true" label="Draw the Silhouette plot from k-min to k-max"/>
        	</when>
        	<when value="dbscan">
        		<conditional name="dbscan_advanced">

31:944e15aa970a

<tool id="MaREA_cluester" name="Cluster Analysis" version="1.0.6">
    <description></description>
    <macros>
        <import>marea_macros.xml</import>
    </macros>
    <requirements>

        	--k_max ${data.k_max}
      	#end if
        ]]>
    </command>
    <inputs>
        <param name="input" argument="--input" type="data" format="tabular, csv, tsv" label="Input dataset" />
        
        <conditional name="data">
			<param name="clust_type" argument="--cluster_type" type="select" label="Choose clustering type:">
                	<option value="kmeans" selected="true">KMeans</option>
                	<option value="dbscan">DBSCAN</option>
                	<option value="hierarchy">Agglomerative Hierarchical</option>
        	</param>
        	<when value="kmeans">
        		<param name="k_min" argument="--k_min" type="integer" min="2" max="20" value="2" label="Min number of clusters (k) to be tested" />
        		<param name="k_max" argument="--k_max" type="integer" min="2" max="20" value="3" label="Max number of clusters (k) to be tested" />
        		<param name="elbow" argument="--elbow" type="boolean" value="true" label="Draw the elbow plot from k-min to k-max"/>
        		<param name="silhouette" argument="--silhouette" type="boolean" value="true" label="Draw the Silhouette plot from k-min to k-max"/>
        	</when>
        	<when value="dbscan">
        		<conditional name="dbscan_advanced">