changeset 20:68c06ccce7bf draft

planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb

--- a/deepTools_macros.xml	Thu Apr 05 10:52:28 2018 -0400
+++ b/deepTools_macros.xml	Mon Jul 09 18:23:50 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@">3.1.0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.0.2">deeptools</requirement>
+            <requirement type="package" version="3.1.0">deeptools</requirement>
             <requirement type="package" version="1.7">samtools</requirement>
         </requirements>
         <expand macro="stdio" />
@@ -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>

--- a/plotCorrelation.xml	Thu Apr 05 10:52:28 2018 -0400
+++ b/plotCorrelation.xml	Mon Jul 09 18:23:50 2018 -0400
@@ -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." />