# HG changeset patch
# User bgruening
# Date 1644571504 0
# Node ID 18ef8e2c9763ebdc685d439eb6bebff4353bf65d
# Parent  2c17ceeae363ea15de572f8e0494139d85e0826b
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit ac42d29c298c026aa0c53c9db2553087ebc86b97"

diff -r 2c17ceeae363 -r 18ef8e2c9763 deepTools_macros.xml
--- a/deepTools_macros.xml	Fri Jan 24 07:40:30 2020 +0000
+++ b/deepTools_macros.xml	Fri Feb 11 09:25:04 2022 +0000
@@ -1,10 +1,10 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">3.3.2.0</token>
+    <token name="@WRAPPER_VERSION@">3.5.1.0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.3.2">deeptools</requirement>
+            <requirement type="package" version="3.5.1">deeptools</requirement>
             <requirement type="package" version="1.9">samtools</requirement>
         </requirements>
         <expand macro="stdio" />
diff -r 2c17ceeae363 -r 18ef8e2c9763 plotCoverage.xml
--- a/plotCoverage.xml	Fri Jan 24 07:40:30 2020 +0000
+++ b/plotCoverage.xml	Fri Feb 11 09:25:04 2022 +0000
@@ -26,7 +26,7 @@
             #end if
 
             #if ' '.join(map(str, $BED)) != 'None':
-                #set bedFileLList=[]
+                #set bedFileList=[]
                 #for $f in $BED:
                     #silent $bedFileList.append("'%s'" % $f)
                 #end for
@@ -101,11 +101,8 @@
                 <expand macro="blacklist" />
             </when>
         </conditional>
-
         <expand macro="input_image_file_format" />
         <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to a file" help=""/>
-
-
     </inputs>
     <outputs>
         <expand macro="output_image_file_format_not_nested" />
diff -r 2c17ceeae363 -r 18ef8e2c9763 repository_dependencies.xml
--- a/repository_dependencies.xml	Fri Jan 24 07:40:30 2020 +0000
+++ b/repository_dependencies.xml	Fri Feb 11 09:25:04 2022 +0000
@@ -1,4 +1,4 @@
 <?xml version="1.0" ?>
 <repositories>
-    <repository changeset_revision="b640d79b49cb" name="data_manager_twobit_builder" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu"/>
+    <repository name="data_manager_twobit_builder" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" changeset_revision="b640d79b49cb"/>
 </repositories>
\ No newline at end of file
diff -r 2c17ceeae363 -r 18ef8e2c9763 test-data/bamPEFragmentSize_result1.txt
--- a/test-data/bamPEFragmentSize_result1.txt	Fri Jan 24 07:40:30 2020 +0000
+++ b/test-data/bamPEFragmentSize_result1.txt	Fri Feb 11 09:25:04 2022 +0000
@@ -12,7 +12,7 @@
 Max.: 251.0
 Std: 4.496912521077347
 MAD: 1.0
-Len. 10%: 241.20000000000002
+Len. 10%: 241.2
 Len. 20%: 241.4
 Len. 30%: 241.6
 Len. 40%: 241.8
diff -r 2c17ceeae363 -r 18ef8e2c9763 test-data/bamPEFragmentSize_table1.txt
--- a/test-data/bamPEFragmentSize_table1.txt	Fri Jan 24 07:40:30 2020 +0000
+++ b/test-data/bamPEFragmentSize_table1.txt	Fri Feb 11 09:25:04 2022 +0000
@@ -1,2 +1,2 @@
 	Frag. Sampled	Frag. Len. Min.	Frag. Len. 1st. Qu.	Frag. Len. Mean	Frag. Len. Median	Frag. Len. 3rd Qu.	Frag. Len. Max	Frag. Len. Std.	Frag. Med. Abs. Dev.	Frag. Len. 10%	Frag. Len. 20%	Frag. Len. 30%	Frag. Len. 40%	Frag. Len. 60%	Frag. Len. 70%	Frag. Len. 80%	Frag. Len. 90%	Frag. Len. 99%	Reads Sampled	Read Len. Min.	Read Len. 1st. Qu.	Read Len. Mean	Read Len. Median	Read Len. 3rd Qu.	Read Len. Max	Read Len. Std.	Read Med. Abs. Dev.	Read Len. 10%	Read Len. 20%	Read Len. 30%	Read Len. 40%	Read Len. 60%	Read Len. 70%	Read Len. 80%	Read Len. 90%	Read Len. 99%
-bowtie2 test1.bam	3	241.0	241.5	244.66666666666666	242.0	246.5	251.0	4.496912521077347	1.0	241.20000000000002	241.4	241.6	241.8	243.8	245.6	247.4	249.2	250.82	3	251.0	251.0	251.0	251.0	251.0	251.0	0.0	0.0	251.0	251.0	251.0	251.0	251.0	251.0	251.0	251.0	251.0
+bowtie2 test1.bam	3	241.0	241.5	244.66666666666666	242.0	246.5	251.0	4.496912521077347	1.0	241.2	241.4	241.6	241.8	243.8	245.6	247.4	249.2	250.82	3	251.0	251.0	251.0	251.0	251.0	251.0	0.0	0.0	251.0	251.0	251.0	251.0	251.0	251.0	251.0	251.0	251.0
diff -r 2c17ceeae363 -r 18ef8e2c9763 test-data/plotFingerprint_quality_metrics.tabular
--- a/test-data/plotFingerprint_quality_metrics.tabular	Fri Jan 24 07:40:30 2020 +0000
+++ b/test-data/plotFingerprint_quality_metrics.tabular	Fri Feb 11 09:25:04 2022 +0000
@@ -1,3 +1,3 @@
 Sample	AUC	Synthetic AUC	X-intercept	Synthetic X-intercept	Elbow Point	Synthetic Elbow Point	JS Distance	Synthetic JS Distance	% genome enriched	diff. enrichment	CHANCE divergence
-bowtie2 test1.bam	0.00493632029863651	0.481650684757865	0.984443061605476	1.1531044350267195e-24	0.9849408836341008	0.5232688298112538	NA	0.26900449806812143	NA	NA	NA
-bowtie2 test1.bam	0.00493632029863651	0.481650684757865	0.984443061605476	1.1531044350267195e-24	0.9849408836341008	0.5232688298112538	0.0	0.26900449806812143	0	0	0
+bowtie2 test1.bam	0.00493632029863651	0.481650684757865	0.984443061605476	1.1531044350267195e-24	0.9849408836341008	0.5232688298112538	nan	0.2690044980681214	nan	nan	nan
+bowtie2 test1.bam	0.00493632029863651	0.481650684757865	0.984443061605476	1.1531044350267195e-24	0.9849408836341008	0.5232688298112538	0.0	0.2690044980681214	0	0	0
diff -r 2c17ceeae363 -r 18ef8e2c9763 test-data/plotPCA_result2.tabular
--- a/test-data/plotPCA_result2.tabular	Fri Jan 24 07:40:30 2020 +0000
+++ b/test-data/plotPCA_result2.tabular	Fri Feb 11 09:25:04 2022 +0000
@@ -1,4 +1,4 @@
 #plotPCA --outFileNameData
 Component	bowtie2-test1.bam	bowtie2-test1.bam	Eigenvalue
 1	-0.7071067811865476	-0.7071067811865475	4.0
-2	-0.7071067811865475	0.7071067811865476	1.2325951644078315e-32
+2	-0.7071067811865475	0.7071067811865476	2.49319462166397e-32