diff heatmapper.xml @ 18:5ea8782d650c draft

Uploaded

--- a/heatmapper.xml	Sat Dec 21 14:26:06 2013 -0500
+++ b/heatmapper.xml	Mon Feb 03 13:44:35 2014 -0500
@@ -1,8 +1,9 @@
-<tool id="deeptools_heatmapper" name="heatmapper" version="1.0.2">
+<tool id="deeptools_heatmapper" name="heatmapper" version="1.0.3">
     <description>creates a heatmap for a score associated to genomic regions</description>
     <expand macro="requirements"/>
     <expand macro="stdio" />
     <macros>
+        <token name="@BINARY@">heatmapper</token>
         <import>deepTools_macros.xml</import>
     </macros>
     <command>
@@ -80,13 +81,7 @@
 
             $advancedOpt.onePlotPerGroup
 
-            #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'yes':
-                #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
-                    #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
-                        --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
-                    #end if
-                #end if
-            #end if
+            @kmeans_clusterin@
 
         #end if
     </command>
@@ -147,7 +142,6 @@
 
                 <param name="whatToShow" type="select" label="What to show" help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar.">
                     <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option>
-                    <option value="plot only">summary plot only</option>
                     <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
                     <option value="heatmap only">heatmap only</option>
                     <option value="heatmap and colorbar">heatmap and colorbar</option>
@@ -171,28 +165,8 @@
                     label="Do one plot per group" 
                     help="When computeMatrix was used on more than one group of genes, the average plots for all the groups will be drawn in one panel by default. If this option is set, each group will get its own plot, stacked on top of each other."/>
 
-                <conditional name="used_multiple_regions">
-                    <param name="used_multiple_regions_options" type="select" 
-                        label="Did you used multiple regions in ComputeMatrix?"
-                        help="That option is only relevant if you want to cluster the results. Clustering is only available with one selected region in ComputeMatrix.">
-                        <option value="no">No, I used only one region.</option>
-                        <option value="yes">Yes, I used multiple regions.</option>
-                    </param>
-                    <when value="yes">
-                        <conditional name="clustering">
-                            <param name="clustering_options" type="select" label="Clustering algorithm">
-                                <option value="none">No clustering</option>
-                                <option value="kmeans">Kmeans clustering</option>
-                            </param>
-                            <when value="kmeans">
-                                <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" 
-                                    help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/>
-                            </when>
-                            <when value="none" />
-                        </conditional>
-                    </when>
-                    <when value="no" />
-                </conditional>
+                <expand macro="kmeans_clustering" />
+
             </when>
         </conditional>
     </inputs>
@@ -224,9 +198,12 @@
    :alt: Heatmap of RNA Polymerase II ChIP-seq
 
 
------
+You can find more details in the `heatmapper wiki`_.
 
-.. class:: infomark
+.. _heatmapper wiki: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-heatmapper
+
+
+-----
 
 @REFERENCES@