# HG changeset patch
# User bgruening
# Date 1534883805 14400
# Node ID 67f3aaf8d49f41a9f61c9e67be59ce2d36b31f83
# Parent  e0be6dd1b73884c3c5857e36aa9d932f7b5b7196
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a

diff -r e0be6dd1b738 -r 67f3aaf8d49f deepTools_macros.xml
--- a/deepTools_macros.xml	Thu Apr 05 10:40:50 2018 -0400
+++ b/deepTools_macros.xml	Tue Aug 21 16:36:45 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 e0be6dd1b738 -r 67f3aaf8d49f plotEnrichment.xml
--- a/plotEnrichment.xml	Thu Apr 05 10:40:50 2018 -0400
+++ b/plotEnrichment.xml	Tue Aug 21 16:36:45 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="deeptools_plot_enrichment" name="plotEnrichment" version="@WRAPPER_VERSION@.0">
+<tool id="deeptools_plot_enrichment" name="plotEnrichment" version="@WRAPPER_VERSION@.0" profile="18.01">
     <description>plots read/fragment coverage over sets of regions</description>
     <macros>
         <token name="@BINARY@">plotEnrichment</token>
diff -r e0be6dd1b738 -r 67f3aaf8d49f test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r e0be6dd1b738 -r 67f3aaf8d49f test-data/plotPCA_result2.png
Binary file test-data/plotPCA_result2.png has changed