# HG changeset patch
# User bgruening
# Date 1535011334 14400
# Node ID e57332b94d4f3efbad8d7447c6dd974af43b0c7d
# Parent  7e55c0415e71245c8571b9759d64d32301157de7
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a

diff -r 7e55c0415e71 -r e57332b94d4f bamCoverage.xml
--- a/bamCoverage.xml	Thu Apr 05 10:45:32 2018 -0400
+++ b/bamCoverage.xml	Thu Aug 23 04:02:14 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 7e55c0415e71 -r e57332b94d4f deepTools_macros.xml
--- a/deepTools_macros.xml	Thu Apr 05 10:45:32 2018 -0400
+++ b/deepTools_macros.xml	Thu Aug 23 04:02:14 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@">3.1.2.0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.0.2">deeptools</requirement>
+            <requirement type="package" version="3.1.2">deeptools</requirement>
             <requirement type="package" version="1.7">samtools</requirement>
         </requirements>
         <expand macro="stdio" />
@@ -216,7 +216,7 @@
             label="Use a metagene model"
             help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." />
         <param argument="--transcriptID" optional="True" value="transcript" type="text"
-            label="trascript designator"
+            label="transcript designator"
             help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as transcripts. Default: transcript" />
         <param argument="--exonID" optional="True" value="exon" type="text"
             label="exon designator"
@@ -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>
@@ -642,7 +654,7 @@
     </xml>
 
     <xml name="output_image_file_format">
-        <data format="png" name="outFileName" label="${tool.name} image">
+        <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
             <change_format>
                 <when input="output.outFileFormat" value="pdf" format="pdf" />
                 <when input="output.outFileFormat" value="svg" format="svg" />
@@ -653,7 +665,7 @@
     </xml>
 
     <xml name="output_image_file_format_not_nested">
-        <data format="png" name="outFileName" label="${tool.name} image">
+        <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
             <change_format>
                 <when input="outFileFormat" value="pdf" format="pdf" />
                 <when input="outFileFormat" value="svg" format="svg" />
diff -r 7e55c0415e71 -r e57332b94d4f test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r 7e55c0415e71 -r e57332b94d4f test-data/plotPCA_result2.png
Binary file test-data/plotPCA_result2.png has changed