# HG changeset patch
# User bgruening
# Date 1450873957 18000
# Node ID a3c0c28d26c6ed2e1a1565e1654bc8e2cf3ea0e1
# Parent  81f8efdc1f7ba6320fd607ad8708c4f944ae7641
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69

diff -r 81f8efdc1f7b -r a3c0c28d26c6 correctGCBias.xml
--- a/correctGCBias.xml	Wed Dec 23 03:58:23 2015 -0500
+++ b/correctGCBias.xml	Wed Dec 23 07:32:37 2015 -0500
@@ -1,5 +1,5 @@
 <tool id="deeptools_correct_gc_bias" name="correctGCBias" version="@WRAPPER_VERSION@.0">
-    <description>uses the output from computeGCBias to generate corrected BAM files</description>
+    <description>uses the output from computeGCBias to generate GC-corrected BAM files</description>
     <macros>
         <token name="@BINARY@">correctGCBias</token>
         <import>deepTools_macros.xml</import>
@@ -59,7 +59,7 @@
 Benjamini and Speed (2012) Nucleic Acids Res.
 The resulting BAM file can be used in any downstream analyses, but be aware that you should not filter out duplicates from here on.
 
-You can find more details on the correctGCBias wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-correctGCbias
+You can find more details on the correctGCBias doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/correctGCBias.html
 
 
 **Output files**:
diff -r 81f8efdc1f7b -r a3c0c28d26c6 deepTools_macros.xml
--- a/deepTools_macros.xml	Wed Dec 23 03:58:23 2015 -0500
+++ b/deepTools_macros.xml	Wed Dec 23 07:32:37 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 81f8efdc1f7b -r a3c0c28d26c6 static/images/plotCorrelation_galaxy_bw_heatmap_output.png
Binary file static/images/plotCorrelation_galaxy_bw_heatmap_output.png has changed
diff -r 81f8efdc1f7b -r a3c0c28d26c6 test-data/bamCoverage_result1.bw
Binary file test-data/bamCoverage_result1.bw has changed
diff -r 81f8efdc1f7b -r a3c0c28d26c6 test-data/bamCoverage_result2.bw
Binary file test-data/bamCoverage_result2.bw has changed
diff -r 81f8efdc1f7b -r a3c0c28d26c6 test-data/bamCoverage_result3.bg
--- a/test-data/bamCoverage_result3.bg	Wed Dec 23 03:58:23 2015 -0500
+++ b/test-data/bamCoverage_result3.bg	Wed Dec 23 07:32:37 2015 -0500
@@ -5,4 +5,4 @@
 chrM	220	230	7690304.31
 chrM	230	240	6027535.81
 chrM	240	250	3325537.00
-chrM	250	260	623538.19
+chrM	250	16569	623538.2
diff -r 81f8efdc1f7b -r a3c0c28d26c6 test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r 81f8efdc1f7b -r a3c0c28d26c6 test-data/profiler_result2.png
Binary file test-data/profiler_result2.png has changed