# HG changeset patch
# User bgruening
# Date 1685630491 0
# Node ID 5be24eba848d8d251289304dde4bf0b4a8cc93fb
# Parent  56d5b797ce8465693222b6bd758c0025db46e77d
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9

diff -r 56d5b797ce84 -r 5be24eba848d computeGCBias.xml
--- a/computeGCBias.xml	Fri Feb 11 15:22:52 2022 +0000
+++ b/computeGCBias.xml	Thu Jun 01 14:41:31 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="deeptools_compute_gc_bias" name="computeGCBias" version="@WRAPPER_VERSION@.0" profile="18.01">
+<tool id="deeptools_compute_gc_bias" name="computeGCBias" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
     <description>Determine the GC bias of your sequenced reads</description>
     <macros>
         <token name="@BINARY@">computeGCBias</token>
diff -r 56d5b797ce84 -r 5be24eba848d deepTools_macros.xml
--- a/deepTools_macros.xml	Fri Feb 11 15:22:52 2022 +0000
+++ b/deepTools_macros.xml	Thu Jun 01 14:41:31 2023 +0000
@@ -1,10 +1,11 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">3.5.1.0</token>
+    <token name="@TOOL_VERSION@">3.5.2</token>
+    <token name="@GALAXY_VERSION@">20.01</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.5.1">deeptools</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">deeptools</requirement>
             <requirement type="package" version="1.9">samtools</requirement>
         </requirements>
         <expand macro="stdio" />
@@ -368,7 +369,6 @@
     <xml name="pseudocount">
         <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@">
 
 .. class:: infomark
@@ -483,7 +483,7 @@
     <token name="@multiple_input_bams@">
 <![CDATA[
         #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
-            #set custom_labels=labels
+            #set custom_labels=$custom_sample_labels_conditional.labels
         #end if
         #set files=[]
         #set labels=[]
@@ -498,7 +498,7 @@
                     ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' &&
                 #end if
                 #silent $files.append("'%s.bam'" % $counter)
-                #silent $labels.append("'%s'" % identifier)
+                #silent $labels.append("'%s'" % $identifier)
             #end for
         #else:
             #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
@@ -522,7 +522,7 @@
     <token name="@multiple_input_bigwigs@">
 <![CDATA[
         #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
-            #set custom_labels=labels
+            #set custom_labels=$custom_sample_labels_conditional.labels
         #end if
         #set files=[]
         #set labels=[]
diff -r 56d5b797ce84 -r 5be24eba848d test-data/bigwigAverage2.bw
Binary file test-data/bigwigAverage2.bw has changed
diff -r 56d5b797ce84 -r 5be24eba848d test-data/multiBigwigSummary_result1.npz
Binary file test-data/multiBigwigSummary_result1.npz has changed
diff -r 56d5b797ce84 -r 5be24eba848d test-data/multiBigwigSummary_result2.npz
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiBigwigSummary_result2.npz	Thu Jun 01 14:41:31 2023 +0000
@@ -0,0 +1,121 @@
+#'chr'	'start'	'end'	'sample1'	'sample2'
+ch1	0	10	0.0	0.0
+ch1	10	20	0.0	0.0
+ch1	20	30	0.0	0.0
+ch1	30	40	0.0	0.0
+ch1	40	50	0.0	0.0
+ch1	50	60	0.0	0.0
+ch1	60	70	0.0	0.0
+ch1	70	80	0.0	0.0
+ch1	80	90	0.0	0.0
+ch1	90	100	0.0	0.0
+ch1	100	110	2.0	2.0
+ch1	110	120	2.0	2.0
+ch1	120	130	1.0	1.0
+ch1	130	140	0.0	0.0
+ch1	140	150	0.0	0.0
+ch1	150	160	0.0	0.0
+ch1	160	170	0.0	0.0
+ch1	170	180	0.0	0.0
+ch1	180	190	0.0	0.0
+ch1	190	200	0.0	0.0
+ch1	200	210	0.0	0.0
+ch1	210	220	0.0	0.0
+ch1	220	230	0.0	0.0
+ch1	230	240	0.0	0.0
+ch1	240	250	0.0	0.0
+ch1	250	260	0.0	0.0
+ch1	260	270	0.0	0.0
+ch1	270	280	0.0	0.0
+ch1	280	290	0.0	0.0
+ch1	290	300	0.0	0.0
+ch1	300	310	0.0	0.0
+ch1	310	320	0.0	0.0
+ch1	320	330	0.0	0.0
+ch1	330	340	0.0	0.0
+ch1	340	350	0.0	0.0
+ch1	350	360	0.0	0.0
+ch1	360	370	0.0	0.0
+ch1	370	380	0.0	0.0
+ch1	380	390	0.0	0.0
+ch1	390	400	0.0	0.0
+ch2	0	10	0.0	0.0
+ch2	10	20	0.0	0.0
+ch2	20	30	0.0	0.0
+ch2	30	40	0.0	0.0
+ch2	40	50	0.0	0.0
+ch2	50	60	3.0	3.0
+ch2	60	70	3.0	3.0
+ch2	70	80	1.5	1.5
+ch2	80	90	0.0	0.0
+ch2	90	100	0.0	0.0
+ch2	100	110	0.0	0.0
+ch2	110	120	0.0	0.0
+ch2	120	130	0.0	0.0
+ch2	130	140	0.0	0.0
+ch2	140	150	0.0	0.0
+ch2	150	160	1.0	1.0
+ch2	160	170	1.0	1.0
+ch2	170	180	0.5	0.5
+ch2	180	190	0.0	0.0
+ch2	190	200	0.0	0.0
+ch2	200	210	0.0	0.0
+ch2	210	220	0.0	0.0
+ch2	220	230	0.0	0.0
+ch2	230	240	0.0	0.0
+ch2	240	250	0.0	0.0
+ch2	250	260	0.0	0.0
+ch2	260	270	0.0	0.0
+ch2	270	280	0.0	0.0
+ch2	280	290	0.0	0.0
+ch2	290	300	0.0	0.0
+ch2	300	310	0.0	0.0
+ch2	310	320	0.0	0.0
+ch2	320	330	0.0	0.0
+ch2	330	340	0.0	0.0
+ch2	340	350	0.0	0.0
+ch2	350	360	0.0	0.0
+ch2	360	370	0.0	0.0
+ch2	370	380	0.0	0.0
+ch2	380	390	0.0	0.0
+ch2	390	400	0.0	0.0
+ch3	0	10	0.0	0.0
+ch3	10	20	0.0	0.0
+ch3	20	30	0.0	0.0
+ch3	30	40	0.0	0.0
+ch3	40	50	0.0	0.0
+ch3	50	60	3.0	3.0
+ch3	60	70	3.0	3.0
+ch3	70	80	1.5	1.5
+ch3	80	90	0.0	0.0
+ch3	90	100	0.0	0.0
+ch3	100	110	0.0	0.0
+ch3	110	120	0.0	0.0
+ch3	120	130	0.0	0.0
+ch3	130	140	0.0	0.0
+ch3	140	150	0.0	0.0
+ch3	150	160	1.0	1.0
+ch3	160	170	1.0	1.0
+ch3	170	180	0.5	0.5
+ch3	180	190	0.0	0.0
+ch3	190	200	0.0	0.0
+ch3	200	210	0.0	0.0
+ch3	210	220	0.0	0.0
+ch3	220	230	0.0	0.0
+ch3	230	240	0.0	0.0
+ch3	240	250	0.0	0.0
+ch3	250	260	0.0	0.0
+ch3	260	270	0.0	0.0
+ch3	270	280	0.0	0.0
+ch3	280	290	0.0	0.0
+ch3	290	300	0.0	0.0
+ch3	300	310	0.0	0.0
+ch3	310	320	0.0	0.0
+ch3	320	330	0.0	0.0
+ch3	330	340	0.0	0.0
+ch3	340	350	0.0	0.0
+ch3	350	360	0.0	0.0
+ch3	360	370	0.0	0.0
+ch3	370	380	0.0	0.0
+ch3	380	390	0.0	0.0
+ch3	390	400	0.0	0.0
diff -r 56d5b797ce84 -r 5be24eba848d test-data/multiBigwigSummary_result2.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiBigwigSummary_result2.tabular	Thu Jun 01 14:41:31 2023 +0000
@@ -0,0 +1,121 @@
+#'chr'	'start'	'end'	'sample1'	'sample2'
+ch1	0	10	0.0	0.0
+ch1	10	20	0.0	0.0
+ch1	20	30	0.0	0.0
+ch1	30	40	0.0	0.0
+ch1	40	50	0.0	0.0
+ch1	50	60	0.0	0.0
+ch1	60	70	0.0	0.0
+ch1	70	80	0.0	0.0
+ch1	80	90	0.0	0.0
+ch1	90	100	0.0	0.0
+ch1	100	110	2.0	2.0
+ch1	110	120	2.0	2.0
+ch1	120	130	1.0	1.0
+ch1	130	140	0.0	0.0
+ch1	140	150	0.0	0.0
+ch1	150	160	0.0	0.0
+ch1	160	170	0.0	0.0
+ch1	170	180	0.0	0.0
+ch1	180	190	0.0	0.0
+ch1	190	200	0.0	0.0
+ch1	200	210	0.0	0.0
+ch1	210	220	0.0	0.0
+ch1	220	230	0.0	0.0
+ch1	230	240	0.0	0.0
+ch1	240	250	0.0	0.0
+ch1	250	260	0.0	0.0
+ch1	260	270	0.0	0.0
+ch1	270	280	0.0	0.0
+ch1	280	290	0.0	0.0
+ch1	290	300	0.0	0.0
+ch1	300	310	0.0	0.0
+ch1	310	320	0.0	0.0
+ch1	320	330	0.0	0.0
+ch1	330	340	0.0	0.0
+ch1	340	350	0.0	0.0
+ch1	350	360	0.0	0.0
+ch1	360	370	0.0	0.0
+ch1	370	380	0.0	0.0
+ch1	380	390	0.0	0.0
+ch1	390	400	0.0	0.0
+ch2	0	10	0.0	0.0
+ch2	10	20	0.0	0.0
+ch2	20	30	0.0	0.0
+ch2	30	40	0.0	0.0
+ch2	40	50	0.0	0.0
+ch2	50	60	3.0	3.0
+ch2	60	70	3.0	3.0
+ch2	70	80	1.5	1.5
+ch2	80	90	0.0	0.0
+ch2	90	100	0.0	0.0
+ch2	100	110	0.0	0.0
+ch2	110	120	0.0	0.0
+ch2	120	130	0.0	0.0
+ch2	130	140	0.0	0.0
+ch2	140	150	0.0	0.0
+ch2	150	160	1.0	1.0
+ch2	160	170	1.0	1.0
+ch2	170	180	0.5	0.5
+ch2	180	190	0.0	0.0
+ch2	190	200	0.0	0.0
+ch2	200	210	0.0	0.0
+ch2	210	220	0.0	0.0
+ch2	220	230	0.0	0.0
+ch2	230	240	0.0	0.0
+ch2	240	250	0.0	0.0
+ch2	250	260	0.0	0.0
+ch2	260	270	0.0	0.0
+ch2	270	280	0.0	0.0
+ch2	280	290	0.0	0.0
+ch2	290	300	0.0	0.0
+ch2	300	310	0.0	0.0
+ch2	310	320	0.0	0.0
+ch2	320	330	0.0	0.0
+ch2	330	340	0.0	0.0
+ch2	340	350	0.0	0.0
+ch2	350	360	0.0	0.0
+ch2	360	370	0.0	0.0
+ch2	370	380	0.0	0.0
+ch2	380	390	0.0	0.0
+ch2	390	400	0.0	0.0
+ch3	0	10	0.0	0.0
+ch3	10	20	0.0	0.0
+ch3	20	30	0.0	0.0
+ch3	30	40	0.0	0.0
+ch3	40	50	0.0	0.0
+ch3	50	60	3.0	3.0
+ch3	60	70	3.0	3.0
+ch3	70	80	1.5	1.5
+ch3	80	90	0.0	0.0
+ch3	90	100	0.0	0.0
+ch3	100	110	0.0	0.0
+ch3	110	120	0.0	0.0
+ch3	120	130	0.0	0.0
+ch3	130	140	0.0	0.0
+ch3	140	150	0.0	0.0
+ch3	150	160	1.0	1.0
+ch3	160	170	1.0	1.0
+ch3	170	180	0.5	0.5
+ch3	180	190	0.0	0.0
+ch3	190	200	0.0	0.0
+ch3	200	210	0.0	0.0
+ch3	210	220	0.0	0.0
+ch3	220	230	0.0	0.0
+ch3	230	240	0.0	0.0
+ch3	240	250	0.0	0.0
+ch3	250	260	0.0	0.0
+ch3	260	270	0.0	0.0
+ch3	270	280	0.0	0.0
+ch3	280	290	0.0	0.0
+ch3	290	300	0.0	0.0
+ch3	300	310	0.0	0.0
+ch3	310	320	0.0	0.0
+ch3	320	330	0.0	0.0
+ch3	330	340	0.0	0.0
+ch3	340	350	0.0	0.0
+ch3	350	360	0.0	0.0
+ch3	360	370	0.0	0.0
+ch3	370	380	0.0	0.0
+ch3	380	390	0.0	0.0
+ch3	390	400	0.0	0.0
diff -r 56d5b797ce84 -r 5be24eba848d test-data/test_compated.bw
Binary file test-data/test_compated.bw has changed
diff -r 56d5b797ce84 -r 5be24eba848d test-data/test_half.bw
Binary file test-data/test_half.bw has changed