# HG changeset patch
# User bgruening
# Date 1534885039 14400
# Node ID 708beeae12958089e07a99b95b3d0e867dc99bb6
# Parent  649590afaedc0c333fe04e7e83d9382edfa91fb5
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a

diff -r 649590afaedc -r 708beeae1295 bamCompare.xml
--- a/bamCompare.xml	Thu Apr 05 10:43:02 2018 -0400
+++ b/bamCompare.xml	Tue Aug 21 16:57:19 2018 -0400
@@ -46,6 +46,7 @@
             #end if
 
             --operation $comparison.type
+            $exactScaling
 
             #if $comparison.type in ['ratio','log2']:
                 --pseudocount $comparison.pseudocount
@@ -145,6 +146,7 @@
             </when>
         </conditional>
 
+        <expand macro="exactScaling" />
         <param name="outFileFormat" type="select" label="Coverage file format">
             <option value="bigwig" selected="true">bigwig</option>
             <option value="bedgraph">bedgraph</option>
diff -r 649590afaedc -r 708beeae1295 deepTools_macros.xml
--- a/deepTools_macros.xml	Thu Apr 05 10:43:02 2018 -0400
+++ b/deepTools_macros.xml	Tue Aug 21 16:57:19 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 649590afaedc -r 708beeae1295 test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r 649590afaedc -r 708beeae1295 test-data/plotPCA_result2.png
Binary file test-data/plotPCA_result2.png has changed