# HG changeset patch
# User bgruening
# Date 1522940255 14400
# Node ID ea8efdcf151fd69637a25d2531ddc7ffeccb1221
# Parent  48d08791d4f20f9297a4719336a666b78e273499
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754

diff -r 48d08791d4f2 -r ea8efdcf151f alignmentSieve.xml
--- a/alignmentSieve.xml	Fri Mar 02 16:37:08 2018 -0500
+++ b/alignmentSieve.xml	Thu Apr 05 10:57:35 2018 -0400
@@ -75,7 +75,7 @@
         #if $BED:
             --BED
             -o '$outFile'
-        #elif str($shift) != "":
+        #elif str($shift) != "" or $ATACshift:
             -o foo.bam &&
             samtools sort -o '$outFile' -T foo.tmp -@ "\${GALAXY_SLOTS:-4}" foo.bam &&
             rm foo.bam
diff -r 48d08791d4f2 -r ea8efdcf151f deepTools_macros.xml
--- a/deepTools_macros.xml	Fri Mar 02 16:37:08 2018 -0500
+++ b/deepTools_macros.xml	Thu Apr 05 10:57:35 2018 -0400
@@ -1,10 +1,10 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">3.0.1</token>
+    <token name="@WRAPPER_VERSION@">3.0.2</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.0.1">deeptools</requirement>
+            <requirement type="package" version="3.0.2">deeptools</requirement>
             <requirement type="package" version="1.7">samtools</requirement>
         </requirements>
         <expand macro="stdio" />
@@ -118,6 +118,7 @@
                 <valid initial="string.letters,string.digits">
                     <add value="|"/>
                     <add value=":"/>
+                    <add value="."/>
                  </valid>
             </sanitizer>
         </param>
@@ -443,7 +444,7 @@
         #if $multibam_conditional.orderMatters == "No":
             #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
                 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
-                ln -s "${bamfile}" "./${counter}.bam" &&
+                ln -s '${bamfile}' './${counter}.bam' &&
                 #if $bamfile.ext == 'bam':
                     ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' &&
                 #else:
@@ -455,7 +456,7 @@
         #else:
             #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
                 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
-                ln -s "${f.bamfiles}" "./${counter}.bam" &&
+                ln -s '${f.bamfiles}' './${counter}.bam' &&
                 #if $f.bamfiles.ext == 'bam':
                     ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' &&
                 #else:
@@ -476,14 +477,14 @@
         #if $multibigwig_conditional.orderMatters == "No":
             #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
                 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
-                ln -f -s "${bigwig}" "${identifier}_${counter}.bw" &&
+                ln -f -s '${bigwig}' '${identifier}_${counter}.bw' &&
                 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
                 #silent $labels.append("'%s'" % $identifier)
             #end for
         #else:
             #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
                 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
-                ln -f -s "${f.bigwigfiles}" "${identifier}_${counter}.bw" &&
+                ln -f -s '${f.bigwigfiles}' '${identifier}_${counter}.bw' &&
                 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
                 #silent $labels.append("'%s'" % $identifier)
             #end for
@@ -556,7 +557,7 @@
     #if $source.ref_source=="history":
         --genome $source.input1
     #else:
-        --genome "$source.input1_2bit.fields.path"
+        --genome '$source.input1_2bit.fields.path'
     #end if
     </token>
 
diff -r 48d08791d4f2 -r ea8efdcf151f test-data/multiBamSummary_result1.npz
Binary file test-data/multiBamSummary_result1.npz has changed
diff -r 48d08791d4f2 -r ea8efdcf151f test-data/multiBamSummary_result2.npz
Binary file test-data/multiBamSummary_result2.npz has changed