# HG changeset patch
# User bgruening
# Date 1534884067 14400
# Node ID 003a830433033f5f3fdb221d3b144d9052aee147
# Parent  1d9d0ef3ab377d2412e40ff1d97015213205350c
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a

diff -r 1d9d0ef3ab37 -r 003a83043303 deepTools_macros.xml
--- a/deepTools_macros.xml	Thu Apr 05 10:41:19 2018 -0400
+++ b/deepTools_macros.xml	Tue Aug 21 16:41:07 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 1d9d0ef3ab37 -r 003a83043303 plotCoverage.xml
--- a/plotCoverage.xml	Thu Apr 05 10:41:19 2018 -0400
+++ b/plotCoverage.xml	Tue Aug 21 16:41:07 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="deeptools_plot_coverage" name="plotCoverage" version="@WRAPPER_VERSION@.0">
+<tool id="deeptools_plot_coverage" name="plotCoverage" version="@WRAPPER_VERSION@.0" profile="18.01">
     <description>assesses the sequencing depth of BAM/CRAM files </description>
     <macros>
         <token name="@BINARY@">plotCoverage</token>
diff -r 1d9d0ef3ab37 -r 003a83043303 test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r 1d9d0ef3ab37 -r 003a83043303 test-data/plotPCA_result2.png
Binary file test-data/plotPCA_result2.png has changed