# HG changeset patch
# User bgruening
# Date 1461529266 14400
# Node ID b319edc108a78062df31e48441fcc90df230a4ef
# Parent  f89672f49f94eb105b2ac80f4f02bda60643e274
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty

diff -r f89672f49f94 -r b319edc108a7 deepTools_macros.xml
--- a/deepTools_macros.xml	Fri Mar 18 08:46:50 2016 -0400
+++ b/deepTools_macros.xml	Sun Apr 24 16:21:06 2016 -0400
@@ -68,16 +68,22 @@
     <xml name="region_limit_operation">
         <param argument="--region" type="text" value=""
             label="Region of the genome to limit the operation to"
-            help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;." />
+            help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;.">
+            <sanitizer>
+                <valid initial="string.letters,string.digits">
+                    <add value="|"/>
+                 </valid>
+            </sanitizer>
+        </param>
     </xml>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">2.2.2</token>
+    <token name="@WRAPPER_VERSION@">2.2.3</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="2.7.10">python</requirement>
             <requirement type="binary">@BINARY@</requirement>
-            <requirement type="package" version="2.2.2">deepTools</requirement>
+            <requirement type="package" version="2.2.3">deepTools</requirement>
             <yield />
         </requirements>
         <expand macro="stdio" />
@@ -302,7 +308,7 @@
     </token>
     <xml name="citations">
         <citations>
-            <citation type="doi">10.1093/nar/gku365</citation>
+            <citation type="doi">10.1093/nar/gkw257</citation>
             <yield />
         </citations>
     </xml>
diff -r f89672f49f94 -r b319edc108a7 multiBamSummary.xml
--- a/multiBamSummary.xml	Fri Mar 18 08:46:50 2016 -0400
+++ b/multiBamSummary.xml	Sun Apr 24 16:21:06 2016 -0400
@@ -16,8 +16,8 @@
             @THREADS@
 
             --outFileName '$outFile'
-            --bamfiles '#echo "' '".join($files)#'
-            --labels '#echo "' '".join($labels)#'
+            --bamfiles #echo " ".join($files)#
+            --labels #echo " ".join($labels)#
 
             #if $outRawCounts:
                 --outRawCounts '$outFileRawCounts'
@@ -85,13 +85,13 @@
     </outputs>
     <tests>
         <test>
-            <param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" />
+            <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
             <param name="modeOpt" value="bins" />
             <param name="binSize" value="10" />
             <output name="outFile" file="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
         </test>
         <test>
-            <param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" />
+            <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
             <param name="modeOpt" value="BED-file" />
             <param name="region_file" value="multiBamSummary_regions.bed" />
             <output name="outFile" file="multiBamSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
diff -r f89672f49f94 -r b319edc108a7 test-data/bowtie2 test1.bam
Binary file test-data/bowtie2 test1.bam has changed
diff -r f89672f49f94 -r b319edc108a7 test-data/bowtie2-test1.bam
Binary file test-data/bowtie2-test1.bam has changed
diff -r f89672f49f94 -r b319edc108a7 test-data/plotCoverage_result1.tabular
--- a/test-data/plotCoverage_result1.tabular	Fri Mar 18 08:46:50 2016 -0400
+++ b/test-data/plotCoverage_result1.tabular	Sun Apr 24 16:21:06 2016 -0400
@@ -1,4 +1,4 @@
-#'chr'	'start'	'end'	'bowtie2-test1.bam'	'bowtie2-test1.bam'
+#'chr'	'start'	'end'	'bowtie2 test1.bam'	'bowtie2 test1.bam'
 chrM	0	1	23.0	23.0
 chrM	1	2	35.0	35.0
 chrM	2	3	35.0	35.0
diff -r f89672f49f94 -r b319edc108a7 test-data/plotFingerprint_result2.tabular
--- a/test-data/plotFingerprint_result2.tabular	Fri Mar 18 08:46:50 2016 -0400
+++ b/test-data/plotFingerprint_result2.tabular	Sun Apr 24 16:21:06 2016 -0400
@@ -1,4 +1,4 @@
-'bowtie2-test1.bam'	'bowtie2-test1.bam'
+'bowtie2 test1.bam'	'bowtie2 test1.bam'
 68	68
 65	65
 61	61