# HG changeset patch
# User bgruening
# Date 1531177598 14400
# Node ID 827fe3df85c3e9f2746a86ab3e3eb7aa53b20912
# Parent  3033c3fba0460e22d94d5b168d66bd07ffa22b6a
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb

diff -r 3033c3fba046 -r 827fe3df85c3 bamCoverage.xml
--- a/bamCoverage.xml	Thu Apr 05 10:58:15 2018 -0400
+++ b/bamCoverage.xml	Mon Jul 09 19:06:38 2018 -0400
@@ -41,6 +41,7 @@
             #if str($region).strip() != '':
                 --region '$region'
             #end if
+            $exactScaling
 
             #if $advancedOpt.showAdvancedOpt == "yes":
                 #if str($advancedOpt.scaleFactor).strip() != '':
@@ -101,6 +102,7 @@
             <option value="bedgraph">bedgraph</option>
         </param>
 
+        <expand macro="exactScaling" />
         <expand macro="region_limit_operation" />
 
         <conditional name="advancedOpt">
diff -r 3033c3fba046 -r 827fe3df85c3 deepTools_macros.xml
--- a/deepTools_macros.xml	Thu Apr 05 10:58:15 2018 -0400
+++ b/deepTools_macros.xml	Mon Jul 09 19:06:38 2018 -0400
@@ -1,10 +1,10 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">3.0.2</token>
+    <token name="@WRAPPER_VERSION@">3.1.0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.0.2">deeptools</requirement>
+            <requirement type="package" version="3.1.0">deeptools</requirement>
             <requirement type="package" version="1.7">samtools</requirement>
         </requirements>
         <expand macro="stdio" />
@@ -603,6 +603,18 @@
                  (default: False)" />
     </xml>
 
+    <xml name="exactScaling">
+        <param argument="--exactScaling" type="boolean" truevalue="--exactScaling" falsevalue="" checked="False"
+            label="Compute an exact scaling factor"
+            help="Compute an exact scaling factor rather than one based on
+                  sampled reads. This is only useful in cases where you are
+                  filtering some alignments out AND this are both rare and
+                  tend to clump together in the genome. In such cases the
+                  region-based sampling employed by deepTools would produce
+                  inaccurate scaling factors. Note that this option results
+                  in the process taking significantly more time to complete." />
+    </xml>
+
     <xml name="input_save_matrix_values">
         <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
     </xml>