# HG changeset patch
# User bgruening
# Date 1534883570 14400
# Node ID 659b08d0c4b117d5e6fd77f74fa198c8b06b5a0a
# Parent  bf98fa19b73a95b12e100f000a22f8eb65c02607
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a

diff -r bf98fa19b73a -r 659b08d0c4b1 deepTools_macros.xml
--- a/deepTools_macros.xml	Thu Apr 05 10:40:20 2018 -0400
+++ b/deepTools_macros.xml	Tue Aug 21 16:32:50 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 bf98fa19b73a -r 659b08d0c4b1 plotCorrelation.xml
--- a/plotCorrelation.xml	Thu Apr 05 10:40:20 2018 -0400
+++ b/plotCorrelation.xml	Tue Aug 21 16:32:50 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="deeptools_plot_correlation" name="plotCorrelation" version="@WRAPPER_VERSION@.0">
+<tool id="deeptools_plot_correlation" name="plotCorrelation" version="@WRAPPER_VERSION@.0" profile="18.01">
     <description>Create a heatmap or scatterplot of correlation scores between different samples </description>
     <macros>
         <token name="@BINARY@">plotCorrelation</token>
@@ -18,8 +18,11 @@
                 --plotHeight $plotting_type.plotHeight
             #else:
                 --plotTitle '$plotting_type.plotTitle'
-                #if str($plotting_type.maxRange) != '':
-                    --maxRange '$plotting_type.maxRange'
+                #if str($plotting_type.xRange) != '':
+                    --xRange '$plotting_type.xRange'
+                #end if
+                #if str($plotting_type.yRange) != '':
+                    --yRange '$plotting_type.yRange'
                 #end if
                 $plotting_type.log1p
             #end if
@@ -47,9 +50,12 @@
             </when>
             <when value="scatterplot">
                 <expand macro="plotTitle" />
-                <param argument="--maxRange" type="integer" value="" optional="true"
-                    label="Maximum Range"
-                    help="Maximum (integer) value for the X and Y axes. The default scales these such that the full range of dots is displayed. If you specify --log1p, please ensure that this value is within the range it will produce." />
+                <param argument="--xRange" type="text" value="" optional="true"
+                    label="X axis range"
+                    help="X axis range, the default scales these such that the full range of dots is displayed. The input should be two integers separated by a space." />
+                <param argument="--yRange" type="text" value="" optional="true"
+                    label="Y axis range"
+                    help="Y axis range, the default scales these such that the full range of dots is displayed. The input should be two integers separated by a space." />
                 <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue=""
                     label="Log transform"
                     help="Plot the natural log of the scatter plot after adding 1. Note that this is ONLY for plotting, the correlation is unaffected." />
diff -r bf98fa19b73a -r 659b08d0c4b1 test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r bf98fa19b73a -r 659b08d0c4b1 test-data/plotPCA_result2.png
Binary file test-data/plotPCA_result2.png has changed