# HG changeset patch
# User bgruening
# Date 1450861187 18000
# Node ID 0da0ae5c854ee3f4c8c3c930096ac00f30b0668c
# Parent  7aa5951c56b77deaf2c7800821cf8edbb512df00
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 54a10cf268ca9a5399f13458a1b218be7891bd41

diff -r 7aa5951c56b7 -r 0da0ae5c854e bamCompare.xml
--- a/bamCompare.xml	Tue Dec 22 13:47:00 2015 -0500
+++ b/bamCompare.xml	Wed Dec 23 03:59:47 2015 -0500
@@ -74,13 +74,13 @@
         <param argument="--bamFile2" format="bam" type="data" label="Second BAM file (e.g. control sample)"
             help="The BAM file must be sorted."/>
 
-        <param argument="--binSize" type="integer" value="50" min="1"
+        <param argument="--binSize" type="integer" value="50" min="1" 
             label="Bin size in bp"
             help="The genome will be divided in bins (also called tiles) of the specified length. For each bin the overlaping number of fragments (or reads) will be reported.
                 If only half a fragment overlaps, this fraction will be reported."/>
 
         <conditional name="scaling">
-            <param name="method" type="select"
+            <param name="method" type="select" 
                 label="Method to use for scaling the largest sample to the smallest">
                 <option value="readCount" selected="true">read count</option>
                 <option value="SES">signal extraction scaling (SES), check the bamFingerprint plot before using it!</option>
@@ -101,7 +101,7 @@
         </conditional>
 
         <conditional name="comparison">
-            <param name="type" type="select"
+            <param name="type" type="select" 
                 label="How to compare the two files"
                 help="The default is to output the log2ratio between the two samples.
                 The reciprocal ratio returns the negative of the inverse of the ratio if
@@ -218,7 +218,7 @@
 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
 
 
-You can find more details on the bamCompare doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/bamCompare.html
+You can find more details on the bamCompare wiki page: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCompare
 
 
 **Output files**:
diff -r 7aa5951c56b7 -r 0da0ae5c854e deepTools_macros.xml
--- a/deepTools_macros.xml	Tue Dec 22 13:47:00 2015 -0500
+++ b/deepTools_macros.xml	Wed Dec 23 03:59:47 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 7aa5951c56b7 -r 0da0ae5c854e static/images/plotCorrelation_galaxy_bw_heatmap_output.png
Binary file static/images/plotCorrelation_galaxy_bw_heatmap_output.png has changed
diff -r 7aa5951c56b7 -r 0da0ae5c854e test-data/bamCoverage_result1.bw
Binary file test-data/bamCoverage_result1.bw has changed
diff -r 7aa5951c56b7 -r 0da0ae5c854e test-data/bamCoverage_result2.bw
Binary file test-data/bamCoverage_result2.bw has changed
diff -r 7aa5951c56b7 -r 0da0ae5c854e test-data/bamCoverage_result3.bg
--- a/test-data/bamCoverage_result3.bg	Tue Dec 22 13:47:00 2015 -0500
+++ b/test-data/bamCoverage_result3.bg	Wed Dec 23 03:59:47 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 7aa5951c56b7 -r 0da0ae5c854e test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r 7aa5951c56b7 -r 0da0ae5c854e test-data/profiler_result2.png
Binary file test-data/profiler_result2.png has changed
diff -r 7aa5951c56b7 -r 0da0ae5c854e tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Dec 22 13:47:00 2015 -0500
+++ b/tool_dependencies.xml	Wed Dec 23 03:59:47 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>