# HG changeset patch
# User bgruening
# Date 1559137405 14400
# Node ID d9114ef1c8a5e3909c236eaf6917f9acbda3dbd0
# Parent  ce4ce3316f74836ba3a21c648851660a41b7bf4e
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9092b83f7ab4d7d57409f0cd9046d573209e9a83

diff -r ce4ce3316f74 -r d9114ef1c8a5 deepTools_macros.xml
--- a/deepTools_macros.xml	Tue Apr 02 08:13:06 2019 -0400
+++ b/deepTools_macros.xml	Wed May 29 09:43:25 2019 -0400
@@ -1,10 +1,10 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">3.2.1.0</token>
+    <token name="@WRAPPER_VERSION@">3.3.0.0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.2.1">deeptools</requirement>
+            <requirement type="package" version="3.3.0">deeptools</requirement>
             <requirement type="package" version="1.9">samtools</requirement>
         </requirements>
         <expand macro="stdio" />
diff -r ce4ce3316f74 -r d9114ef1c8a5 plotEnrichment.xml
--- a/plotEnrichment.xml	Tue Apr 02 08:13:06 2019 -0400
+++ b/plotEnrichment.xml	Wed May 29 09:43:25 2019 -0400
@@ -29,6 +29,10 @@
             #end if
 
             #if $advancedOpt.showAdvancedOpt == "yes"
+                #if $advancedOpt.attributeKey:
+                    --attributeKey '$advancedOpt.attributeKey'
+                #end if
+
                 #if $advancedOpt.labels and str($advancedOpt.labels).strip() != "":
                     --labels $advancedOpt.labels
                 #end if
@@ -84,6 +88,11 @@
         <expand macro="input_image_file_format" />
 
         <expand macro="advancedOpt_scaffold">
+            <param argument="--attributeKey" type="text" optional="true" label="Optional attribute key"
+                help="Instead of deriving the feature label from the feature column, use the value of the given
+                attribute key. For example, the gene_biotype. Note that 'None' is used for BED files
+                or entries where the attributeKey is not found." />
+
             <param argument="--plotHeight" type="integer" value="20" min="3"
                 label="Plot height"
                 help="Height in cm. The default for the plot height is 20 centimeters. The minimum value is 3 cm." />
diff -r ce4ce3316f74 -r d9114ef1c8a5 test-data/plotCoverage.metrics
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotCoverage.metrics	Wed May 29 09:43:25 2019 -0400
@@ -0,0 +1,9 @@
+Sample	Threshold	Percent
+bowtie2 test1.bam	0	100.000
+bowtie2 test1.bam	0	100.000
+bowtie2 test1.bam	5	 1.509
+bowtie2 test1.bam	5	 1.509
+bowtie2 test1.bam	10	 1.461
+bowtie2 test1.bam	10	 1.461
+bowtie2 test1.bam	20	 1.406
+bowtie2 test1.bam	20	 1.406
diff -r ce4ce3316f74 -r d9114ef1c8a5 test-data/plotCoverage_result1.png
Binary file test-data/plotCoverage_result1.png has changed