# HG changeset patch
# User iuc
# Date 1579370377 18000
# Node ID 8b62f89924a7aa30d5da4d58a1bac92a3276b077
# Parent  fe3fe68b09a7afb0946bbc96b642c0e835c06965
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 64bbe6ec9a3f3cd6241fa4cf0e0548e0e67629a0"

diff -r fe3fe68b09a7 -r 8b62f89924a7 macros.xml
--- a/macros.xml	Fri May 24 13:30:30 2019 -0400
+++ b/macros.xml	Sat Jan 18 12:59:37 2020 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">0.3.3</token>
+    <token name="@TOOL_VERSION@">0.4.1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">slamdunk</requirement>
@@ -29,7 +29,7 @@
     </xml>
     <xml name="citations">
         <citation type="doi">
-			10.1186/s12859-019-2849-7
+            10.1186/s12859-019-2849-7
         </citation>
     </xml>
-</macros>
\ No newline at end of file
+</macros>
diff -r fe3fe68b09a7 -r 8b62f89924a7 slamdunk.xml
--- a/slamdunk.xml	Fri May 24 13:30:30 2019 -0400
+++ b/slamdunk.xml	Sat Jan 18 12:59:37 2020 -0500
@@ -125,7 +125,7 @@
             </output_collection>
             <output_collection name="outputTsv">
                 <element name="reads_slamdunk_mapped_filtered" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv"
-                lines_diff="2"  />
+                compare="re_match"  />
             </output_collection>
             <output_collection name="outputVcf">
                 <element name="reads_slamdunk_mapped_filtered" ftype="vcf" file="reads1_snp.vcf" compare="sim_size" />
@@ -134,6 +134,7 @@
         <test>
             <!--Ensure built-in fasta works -->
             <param name="reference_source_selector" value="cached" />
+            <param name="ref_file" value="hg38full" />
             <param name="Reference" value="actb.bed" />
             <param name="reads" ftype="fastqsanger" dbkey="hg38" value="reads.fq" />
             <param name="readLength" value="100" />
@@ -148,7 +149,7 @@
             </output_collection>
             <output_collection name="outputTsv">
                 <element name="reads_slamdunk_mapped_filtered" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv"
-                lines_diff="2"  />
+                compare="re_match"  />
             </output_collection>
             <output_collection name="outputVcf">
                 <element name="reads_slamdunk_mapped_filtered" ftype="vcf" file="reads1_snp.vcf" compare="sim_size" />
diff -r fe3fe68b09a7 -r 8b62f89924a7 test-data/reads1_overallrates.csv
--- a/test-data/reads1_overallrates.csv	Fri May 24 13:30:30 2019 -0400
+++ b/test-data/reads1_overallrates.csv	Sat Jan 18 12:59:37 2020 -0500
@@ -1,4 +1,4 @@
-# slamdunk rates v0.3.3
+# slamdunk rates v0.4.1
 	A	a	C	c	G	g	T	t	N	n	
 A	93	20	0	0	0	1	0	0	0	0	
 C	0	0	106	12	0	0	0	0	0	0	
diff -r fe3fe68b09a7 -r 8b62f89924a7 test-data/reads_slamdunk_mapped_filtered_tcount.tsv
--- a/test-data/reads_slamdunk_mapped_filtered_tcount.tsv	Fri May 24 13:30:30 2019 -0400
+++ b/test-data/reads_slamdunk_mapped_filtered_tcount.tsv	Sat Jan 18 12:59:37 2020 -0500
@@ -1,2 +1,4 @@
+#slamdunk v0.4.1	3	sample info:	sample_0	0	NA	-1
+#annotation:	dataset_.*.dat	.*
 Chromosome	Start	End	Name	Length	Strand	ConversionRate	ReadsCPM	Tcontent	CoverageOnTs	ConversionsOnTs	ReadCount	TcReadCount	multimapCount	ConversionRateLower	ConversionRateUpper
-chr5	120498	122492	Actb	1994	+	0.0222222222222	666666.666667	445	90	2	8	4	0	-1.0	-1.0
+chr5	120498	122492	Actb	1994	\+	0.022\d*	666666.66\d*	445	90	2	8	4	0	-1\.0	-1\.0
diff -r fe3fe68b09a7 -r 8b62f89924a7 test-data/summary.txt
--- a/test-data/summary.txt	Fri May 24 13:30:30 2019 -0400
+++ b/test-data/summary.txt	Sat Jan 18 12:59:37 2020 -0500
@@ -1,4 +1,4 @@
-# slamdunk summary v0.3.3
+# slamdunk summary v0.4.1
 FileName	SampleName	SampleType	SampleTime	Sequenced	Mapped	Deduplicated	MQ-Filtered	Identity-Filtered	NM-Filtered	Multimap-Filtered	Retained	Counted	Annotation
 ./filter/reads1.bam	sample_1	NA	-1	12	12	0	0	0	0	0	12	16	
 ./filter/reads2.bam	sample_2	NA	-1	6	6	0	0	0	0	0	6	12