# HG changeset patch
# User bgruening
# Date 1550528517 18000
# Node ID a1a84914d00d6f396dbcb861a3172559f2da4a46
# Parent  89c5b63a954d5e383c5dfcf233fa2e96f3f51b8d
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d

diff -r 89c5b63a954d -r a1a84914d00d deepTools_macros.xml
--- a/deepTools_macros.xml	Tue Aug 21 16:28:32 2018 -0400
+++ b/deepTools_macros.xml	Mon Feb 18 17:21:57 2019 -0500
@@ -1,11 +1,11 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">3.1.2.0</token>
+    <token name="@WRAPPER_VERSION@">3.2.0.0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.1.2">deeptools</requirement>
-            <requirement type="package" version="1.7">samtools</requirement>
+            <requirement type="package" version="3.2.0">deeptools</requirement>
+            <requirement type="package" version="1.9">samtools</requirement>
         </requirements>
         <expand macro="stdio" />
         <version_command>@BINARY@ --version</version_command>
@@ -359,7 +359,7 @@
     </xml>
 
     <xml name="pseudocount">
-        <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
+        <param argument="--pseudocount" type="text" value="1 1" label="Pseudocount" help="Small number to avoid dividing by zero. You can specify separate values for the pseudocount added to the numerator and denominator by providing two values separated by a space."/>
     </xml>
 
     <token name="@REFERENCES@">
@@ -423,12 +423,47 @@
         </conditional>
     </xml>
 
+    <xml name="custom_sample_labels">
+	<conditional name="custom_sample_labels_conditional">
+        <param name="custom_labels_select" type="select" label="Would you like custom sample labels?" help="By default, the names of the samples in your history are used.">
+	    <option value="No" selected="true">No, use sample names in the history</option>
+	    <option value="Yes">Yes, I want to specify new labels</option>
+	</param>
+	<when value="No">
+	</when>
+	<when value="Yes">
+	    <param argument="--labels" type="text" label="Sample Labels" help="Labels, separated by a space. If your labels themselves contain spaces then please enclose them in quotes (e.g., &quot;sample 1&quot; &quot;sample 2&quot;)">
+                <sanitizer>
+                    <valid initial="string.printable">
+                    </valid>
+                </sanitizer>
+            </param>
+	</when>
+        </conditional>
+    </xml>
+
     <xml name="plotTitle">
         <param argument="--plotTitle" type="text" value="" size="30" optional="True"
             label="Title of the plot"
             help="Title of the plot, to be printed on top of the generated image." />
     </xml>
 
+    <xml name="legendLocation">
+        <param argument="--legendLocation" type="select" label="Legend location" help="Location for the legend in the summary plot. Note that none cannot be used in plotProfile.">
+            <option value="best" selected="true">Best (automatic)</option>
+            <option value="upper-right">upper-right</option>
+            <option value="upper-left">upper-left</option>
+            <option value="upper-center">upper-center</option>
+            <option value="lower-right">lower-right</option>
+            <option value="lower-left">lower-left</option>
+            <option value="lower-center">lower-center</option>
+            <option value="center-right">center-right</option>
+            <option value="center-left">center-left</option>
+            <option value="center">center</option>
+            <option value="none">none (only works for heatmaps</option>
+        </param>
+    </xml>
+
     <xml name="labelRotation">
         <param argument="--labelRotation" type="integer" value="0"
             label="Rotation of the X-axis labels (in degrees)"
@@ -438,6 +473,9 @@
 
     <token name="@multiple_input_bams@">
 <![CDATA[
+        #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
+            #set custom_labels=labels
+        #end if
         #set files=[]
         #set labels=[]
         #import re
@@ -466,11 +504,17 @@
                 #silent $labels.append("'%s'" % $identifier)
             #end for
         #end if
+        #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
+            #set labels=custom_labels
+        #end if
 ]]>
     </token>
 
     <token name="@multiple_input_bigwigs@">
 <![CDATA[
+        #if $custom_labels_conditional.custom_labels_select == "Yes":
+            #set custom_labels=labels
+        #end if
         #set files=[]
         #set labels=[]
         #import re
@@ -489,6 +533,9 @@
                 #silent $labels.append("'%s'" % $identifier)
             #end for
         #end if
+        #if $custom_labels_conditional.custom_labels_select == "Yes":
+            #set labels=custom_labels
+        #end if
 ]]>
     </token>
 
diff -r 89c5b63a954d -r a1a84914d00d multiBamSummary.xml
--- a/multiBamSummary.xml	Tue Aug 21 16:28:32 2018 -0400
+++ b/multiBamSummary.xml	Mon Feb 18 17:21:57 2019 -0500
@@ -23,6 +23,10 @@
                 --outRawCounts '$outFileRawCounts'
             #end if
 
+            #if $scalingFactors:
+                --scalingFactors '$scalingFactorsFile'
+            #end if
+
             #if $mode.modeOpt == "bins":
                 --binSize '$mode.binSize'
                 --distanceBetweenBins '$mode.distanceBetweenBins'
@@ -44,6 +48,7 @@
 
     <inputs>
         <expand macro="multiple_input_bams" MIN="2"/>
+        <expand macro="custom_sample_labels" />
 
         <conditional name="mode">
             <param name="modeOpt" type="select" label="Choose computation mode"
@@ -79,6 +84,7 @@
         </expand>
 
         <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to file" help=""/>
+        <param argument="--scalingFactors" type="boolean" label="Save scaling factors" help="Scaling factors calculated as in DESeq2 and made directly compatible with bamCoverage."/>
 
     </inputs>
     <outputs>
@@ -86,6 +92,9 @@
         <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
             <filter>outRawCounts is True</filter>
         </data>
+        <data format="tabular" name="scalingFactorsFile" label="${tool.name} on ${on_string}: scaling factors">
+            <filter>scalingFactors is True</filter>
+        </data>
     </outputs>
     <tests>
         <test>
diff -r 89c5b63a954d -r a1a84914d00d repository_dependencies.xml
--- a/repository_dependencies.xml	Tue Aug 21 16:28:32 2018 -0400
+++ b/repository_dependencies.xml	Mon Feb 18 17:21:57 2019 -0500
@@ -1,4 +1,4 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ?>
 <repositories>
-    <repository changeset_revision="fced964b054a" name="data_manager_twobit_builder" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-</repositories>
+    <repository changeset_revision="fced964b054a" name="data_manager_twobit_builder" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu"/>
+</repositories>
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