# HG changeset patch
# User bgruening
# Date 1684485240 0
# Node ID d8c919d26d0e138555eb336474559743574e8388
# Parent  e5a296ce8fbbb34fa45cf89b8892ce8d3dc0edee
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit e7e3025eb4fffe5deb34c12a6d402d79241d9ed5

diff -r e5a296ce8fbb -r d8c919d26d0e alignmentSieve.xml
--- a/alignmentSieve.xml	Fri Feb 11 16:01:39 2022 +0000
+++ b/alignmentSieve.xml	Fri May 19 08:34:00 2023 +0000
@@ -136,7 +136,7 @@
             <param name="bamfile" value="paired_chr2L.bam" ftype="bam" />
             <param name="minMappingQuality" value="10" />
             <param name="filterMetrics" value="True" />
-            <output name="outFile" file="alignmentSieve.bam" ftype="bam" />
+            <output name="outFile" file="alignmentSieve.bam" ftype="bam" lines_diff="1" />
             <output name="filterMetricsFile" file="alignmentSieve.txt" ftype="tabular" />
         </test>
         <test>
@@ -150,13 +150,13 @@
             <param name="bamfile" value="paired_chr2L.bam" ftype="bam" />
             <param name="minMappingQuality" value="10" />
             <param name="shift" value="1 -2 3 -4" />
-            <output name="outFile" file="alignmentSieve2.bam" ftype="bam" />
+            <output name="outFile" file="alignmentSieve2.bam" ftype="bam" lines_diff="2" />
         </test>
         <test>
             <param name="bamfile" value="paired_chr2L.cram" ftype="cram" />
             <param name="minMappingQuality" value="10" />
             <param name="shift" value="1 -2 3 -4" />
-            <output name="outFile" file="alignmentSieve3.bam" ftype="bam" />
+            <output name="outFile" file="alignmentSieve3.bam" ftype="bam" lines_diff="2" />
         </test>
     </tests>
 
diff -r e5a296ce8fbb -r d8c919d26d0e deepTools_macros.xml
--- a/deepTools_macros.xml	Fri Feb 11 16:01:39 2022 +0000
+++ b/deepTools_macros.xml	Fri May 19 08:34:00 2023 +0000
@@ -368,7 +368,6 @@
     <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 +482,7 @@
     <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 +497,7 @@
                     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 +521,7 @@
     <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 e5a296ce8fbb -r d8c919d26d0e test-data/bigwigAverage2.bw
Binary file test-data/bigwigAverage2.bw has changed
diff -r e5a296ce8fbb -r d8c919d26d0e test-data/multiBigwigSummary_result1.npz
Binary file test-data/multiBigwigSummary_result1.npz has changed
diff -r e5a296ce8fbb -r d8c919d26d0e test-data/multiBigwigSummary_result2.npz
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiBigwigSummary_result2.npz	Fri May 19 08:34:00 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 e5a296ce8fbb -r d8c919d26d0e test-data/multiBigwigSummary_result2.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiBigwigSummary_result2.tabular	Fri May 19 08:34:00 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 e5a296ce8fbb -r d8c919d26d0e test-data/test_compated.bw
Binary file test-data/test_compated.bw has changed
diff -r e5a296ce8fbb -r d8c919d26d0e test-data/test_half.bw
Binary file test-data/test_half.bw has changed