# HG changeset patch
# User bgruening
# Date 1684485430 0
# Node ID d580d6acd1df773d05e62bb829ec23e01d85e964
# Parent  459cfa861f0bfc149e5479d8504bb5b4a65b6611
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit e7e3025eb4fffe5deb34c12a6d402d79241d9ed5

diff -r 459cfa861f0b -r d580d6acd1df deepTools_macros.xml
--- a/deepTools_macros.xml	Fri Feb 11 16:20:11 2022 +0000
+++ b/deepTools_macros.xml	Fri May 19 08:37:10 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 459cfa861f0b -r d580d6acd1df multiBigwigSummary.xml
--- a/multiBigwigSummary.xml	Fri Feb 11 16:20:11 2022 +0000
+++ b/multiBigwigSummary.xml	Fri May 19 08:37:10 2023 +0000
@@ -1,17 +1,16 @@
-<tool id="deeptools_multi_bigwig_summary" name="multiBigwigSummary" version="@WRAPPER_VERSION@.0">
+<tool id="deeptools_multi_bigwig_summary" name="multiBigwigSummary" version="@WRAPPER_VERSION@.1">
     <description>calculates average scores for a list of two or more bigwig files</description>
     <macros>
         <token name="@BINARY@">multiBigwigSummary</token>
         <import>deepTools_macros.xml</import>
     </macros>
-   <expand macro="requirements" />
+    <expand macro="requirements" />
     <command>
 <![CDATA[
         #set files=[]
         #set labels=[]
 
         @multiple_input_bigwigs@
-
         @BINARY@
             $mode.modeOpt
 
@@ -20,8 +19,10 @@
             --outFileName $outFile
 
             --bwfiles #echo ' '.join($files)#
-            --labels #echo ' '.join($labels)#
-
+            
+            #if $custom_sample_labels_conditional.custom_labels_select == 'Yes'
+                --labels #echo ' '.join($custom_sample_labels_conditional.labels)#
+            #end if
             #if $outRawCounts:
                 --outRawCounts '$outFileRawCounts'
             #end if
@@ -43,7 +44,6 @@
             #end if
 ]]>
     </command>
-
     <inputs>
         <expand macro="multiple_input_bigwigs" MIN="2" LABEL="Bigwig files" TITLE="BigWig files"/>
         <expand macro="custom_sample_labels" />
@@ -70,7 +70,6 @@
                     help="Correlation is computed for the number of reads that overlap such regions."/>
             </when>
         </conditional>
-
         <expand macro="region_limit_operation" />
         <param argument="--outRawCounts" type="boolean" label="Save raw counts (scores) to file" help=""/>
 
@@ -91,18 +90,20 @@
             <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" />
             <param name="modeOpt" value="bins" />
             <param name="binSize" value="10" />
-            <param name="corMethod" value="spearman" />
             <output name="outFile" file="multiBigwigSummary_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
         </test>
-        <!--test>
+        <test>
             <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" />
-            <param name="modeOpt" value="BED-file" />
-            <param name="region_file" value="multiBamSummary_regions.bed" />
-            <param name="corMethod" value="pearson" />
+            <param name="modeOpt" value="bins" />
+            <param name="binSize" value="10" />
             <param name="outRawCounts" value="True" />
+            <conditional name="custom_sample_labels_conditional">
+                <param name="custom_labels_select" value="Yes"/>
+                <param name="labels" value="sample1 sample2"/>
+            </conditional>
             <output name="outFileRawCounts" file="multiBigwigSummary_result2.tabular" ftype="tabular" />
-            <output name="outFileName" file="multiBigwigSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
-        </test-->
+            <output name="outFile" file="multiBigwigSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r 459cfa861f0b -r d580d6acd1df test-data/bigwigAverage2.bw
Binary file test-data/bigwigAverage2.bw has changed
diff -r 459cfa861f0b -r d580d6acd1df test-data/multiBigwigSummary_result1.npz
Binary file test-data/multiBigwigSummary_result1.npz has changed
diff -r 459cfa861f0b -r d580d6acd1df test-data/multiBigwigSummary_result2.npz
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiBigwigSummary_result2.npz	Fri May 19 08:37:10 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 459cfa861f0b -r d580d6acd1df test-data/multiBigwigSummary_result2.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiBigwigSummary_result2.tabular	Fri May 19 08:37:10 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 459cfa861f0b -r d580d6acd1df test-data/test_compated.bw
Binary file test-data/test_compated.bw has changed
diff -r 459cfa861f0b -r d580d6acd1df test-data/test_half.bw
Binary file test-data/test_half.bw has changed