# HG changeset patch
# User bgruening
# Date 1450860750 18000
# Node ID e9e05e3b69fda4939b54b5c2bf603f9460702567
# Parent  841ade9fb78441d4ffa4335178fd6da68556888b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 54a10cf268ca9a5399f13458a1b218be7891bd41

diff -r 841ade9fb784 -r e9e05e3b69fd bigwigCorrelate.xml
--- a/bigwigCorrelate.xml	Tue Dec 22 13:39:43 2015 -0500
+++ b/bigwigCorrelate.xml	Wed Dec 23 03:52:30 2015 -0500
@@ -1,9 +1,9 @@
 <tool id="deeptools_bigwig_correlate" name="bigwigCorrelate" version="@WRAPPER_VERSION@.0">
-    <description>calculates average read coverages for a list of two or more bigwig files</description>
+    <description>correlates pairs of 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)"/>
 
@@ -96,18 +96,19 @@
 <![CDATA[
 **What it does**
 
-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.
+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.
 
 
 **Output files**:
 
-- **Coverage scores**: Coverage scores computed and saved in a format detected by 'plotCorrelation' or 'plotPCA' tools.
+- **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
 
-- 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 841ade9fb784 -r e9e05e3b69fd deepTools_macros.xml
--- a/deepTools_macros.xml	Tue Dec 22 13:39:43 2015 -0500
+++ b/deepTools_macros.xml	Wed Dec 23 03:52:30 2015 -0500
@@ -40,10 +40,10 @@
     </xml>
 
     <token name="@HEATMAP_OPTIONS@">
-        #if str($plotting_type.zMin) != "":
+        #if $plotting_type.zMin:
             --zMin $plotting_type.zMin
         #end if
-        #if str($plotting_type.zMax) != "":
+        #if $plotting_type.zMax:
             --zMax $plotting_type.zMax
         #end if
         --colorMap '$plotting_type.colorMap'
@@ -107,11 +107,7 @@
                     </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: 0 [do not cluster])."/>
+                            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>
@@ -412,6 +408,7 @@
             <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>
@@ -459,6 +456,14 @@
     </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 841ade9fb784 -r e9e05e3b69fd static/images/plotCorrelation_galaxy_bw_heatmap_output.png
Binary file static/images/plotCorrelation_galaxy_bw_heatmap_output.png has changed
diff -r 841ade9fb784 -r e9e05e3b69fd test-data/bamCoverage_result1.bw
Binary file test-data/bamCoverage_result1.bw has changed
diff -r 841ade9fb784 -r e9e05e3b69fd test-data/bamCoverage_result2.bw
Binary file test-data/bamCoverage_result2.bw has changed
diff -r 841ade9fb784 -r e9e05e3b69fd test-data/bamCoverage_result3.bg
--- a/test-data/bamCoverage_result3.bg	Tue Dec 22 13:39:43 2015 -0500
+++ b/test-data/bamCoverage_result3.bg	Wed Dec 23 03:52:30 2015 -0500
@@ -5,4 +5,4 @@
 chrM	220	230	7690304.31
 chrM	230	240	6027535.81
 chrM	240	250	3325537.00
-chrM	250	16569	623538.2
+chrM	250	260	623538.19
diff -r 841ade9fb784 -r e9e05e3b69fd test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r 841ade9fb784 -r e9e05e3b69fd test-data/profiler_result2.png
Binary file test-data/profiler_result2.png has changed
diff -r 841ade9fb784 -r e9e05e3b69fd tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Dec 22 13:39:43 2015 -0500
+++ b/tool_dependencies.xml	Wed Dec 23 03:52:30 2015 -0500
@@ -4,6 +4,6 @@
         <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="deepTools" version="2.0">
-        <repository changeset_revision="747571992679" name="package_python_2_7_deeptools_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="bd40c0aa7d8e" name="package_python_2_7_deeptools_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>