# HG changeset patch
# User bgruening
# Date 1450809583 18000
# Node ID 841ade9fb78441d4ffa4335178fd6da68556888b
# Parent  bdd6ace83c8077ea66c30e34ab21fc0d3765d002
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 8b9cdb8dc4a8fedd2b2286e7afab6529e49a9d22-dirty

diff -r bdd6ace83c80 -r 841ade9fb784 bigwigCorrelate.xml
--- a/bigwigCorrelate.xml	Mon Dec 21 19:01:28 2015 -0500
+++ b/bigwigCorrelate.xml	Tue Dec 22 13:39:43 2015 -0500
@@ -1,9 +1,9 @@
 <tool id="deeptools_bigwig_correlate" name="bigwigCorrelate" version="@WRAPPER_VERSION@.0">
-    <description>correlates pairs of BigWig files</description>
+    <description>calculates average read coverages for a list of two or more bigwig files</description>
     <macros>
         <token name="@BINARY@">bigwigCorrelate</token>
         <import>deepTools_macros.xml</import>
-    </macros> 
+    </macros>
    <expand macro="requirements" />
     <command>
 <![CDATA[
@@ -22,7 +22,7 @@
             --labels '#echo "' '".join($labels)#'
 
             #if $outRawCounts:
-                --outRawCounts '$outFileRawCounts' 
+                --outRawCounts '$outFileRawCounts'
             #end if
 
             #if $mode.modeOpt == "bins":
@@ -42,7 +42,7 @@
         <expand macro="multiple_input_bigwigs" />
 
         <conditional name="mode">
-            <param name="modeOpt" type="select" label="Choose computation mode" 
+            <param name="modeOpt" type="select" label="Choose computation mode"
                 help="In the bins mode, the correlation is computed based on equal length bins.
                 In the BED file mode, as list of genomic regions in BED format has to be given.
                 For each region in the BED file the number of overlapping reads is counted in
@@ -51,7 +51,7 @@
                 <option value="BED-file">Limit correlation to certain regions (BED file)</option>
             </param>
             <when value="bins">
-                <param name="binSize" type="integer" value="10000" min="1" 
+                <param name="binSize" type="integer" value="10000" min="1"
                     label="Bin size in bp"
                     help="Length in base pairs for a window used to sample the genome. (--binSize)"/>
 
@@ -96,19 +96,18 @@
 <![CDATA[
 **What it does**
 
-bigwigCorrelate computes the overall similarity between two or more bigWig
-files based on coverage means of genomic regions. The correlation analysis
-is performed for the entire genome by running the program in 'bins' mode,
-or for certain regions only in 'BED-file' mode. Pearson or Spearman analyses
-are available to compute correlation coefficients. Results are saved to a
-heat map file. Further output files are optional.
+Given two or more bigWig files, bigwigCorrelate computes the average scores for each of the files in every genomic region.
+This analysis is performed for the entire genome by running the program in 'bins' mode, or for certain user selected regions
+in 'BED-file' mode. Most commonly, the output of bigwigCorrelate is used by other tools such as 'plotCorrelation' or 'plotPCA'
+for visualization and diagnostic purposes.
 
 
 **Output files**:
 
-- **diagnostic plot**: clustered heatmap displaying the values for each pair-wise correlation
-- data matrix (optional): if you want to plot the correlation values using a different program, e.g. R, this matrix can be used
+- **Coverage scores**: Coverage scores computed and saved in a format detected by 'plotCorrelation' or 'plotPCA' tools.
 
+- Data matrix (optional,select to save raw counts to a file above): If you want to have a look at the coverage values
+  or compute statistics yourself using a different program (like R).
 
 -----
 
diff -r bdd6ace83c80 -r 841ade9fb784 deepTools_macros.xml
--- a/deepTools_macros.xml	Mon Dec 21 19:01:28 2015 -0500
+++ b/deepTools_macros.xml	Tue Dec 22 13:39:43 2015 -0500
@@ -40,10 +40,10 @@
     </xml>
 
     <token name="@HEATMAP_OPTIONS@">
-        #if $plotting_type.zMin:
+        #if str($plotting_type.zMin) != "":
             --zMin $plotting_type.zMin
         #end if
-        #if $plotting_type.zMax:
+        #if str($plotting_type.zMax) != "":
             --zMax $plotting_type.zMax
         #end if
         --colorMap '$plotting_type.colorMap'
@@ -107,7 +107,11 @@
                     </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)."/>
+                            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: 0 [do not cluster])."/>
                     </when>
                     <when value="none" />
                 </conditional>
@@ -408,7 +412,6 @@
             <when value="no" />
             <when value="yes">
                 <yield />
-                <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
                 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
             </when>
         </conditional>
@@ -456,14 +459,6 @@
     </xml>
 
     <xml name="output_graphic_outputs">
-        <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
-            <filter>
-            ((
-                output['showOutputSettings'] == 'yes' and
-                output['saveData'] is True
-            ))
-            </filter>
-        </data>
         <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
             <filter>
             ((
diff -r bdd6ace83c80 -r 841ade9fb784 static/images/plotCorrelation_galaxy_bw_heatmap_output.png
Binary file static/images/plotCorrelation_galaxy_bw_heatmap_output.png has changed