# HG changeset patch
# User iuc
# Date 1597743595 14400
# Node ID 438f65cb1d1498973f61bca8d10e906a83854746
# Parent  ade773848c3dfbd67dccfaaeacd1b5d6485d1619
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 7f117678cfee55bb18706fd1bf14c0a380261eab"

diff -r ade773848c3d -r 438f65cb1d14 repeatmasker.xml
--- a/repeatmasker.xml	Thu Jan 23 04:40:29 2020 -0500
+++ b/repeatmasker.xml	Tue Aug 18 05:39:55 2020 -0400
@@ -1,12 +1,12 @@
-<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.7+galaxy2" profile="17.01">
+<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.9" profile="17.01">
   <description>screen DNA sequences for interspersed repeats and low complexity regions</description>
 
   <requirements>
-    <requirement type="package" version="4.0.7">repeatmasker</requirement>
+    <requirement type="package" version="4.0.9_p2">repeatmasker</requirement>
   </requirements>
 
   <command detect_errors="exit_code"><![CDATA[
-    RM_PATH=\$(which RepeatMasker) && 
+    RM_PATH=\$(which RepeatMasker) &&
     if [ -z "\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\$PATH)" >&2 ; exit 1 ; fi &&
     RM_LIB_PATH=\$(dirname \$RM_PATH)/../share/RepeatMasker/Libraries &&
     mkdir lib &&
diff -r ade773848c3d -r 438f65cb1d14 test-data/small.fasta.cat
--- a/test-data/small.fasta.cat	Thu Jan 23 04:40:29 2020 -0500
+++ b/test-data/small.fasta.cat	Tue Aug 18 05:39:55 2020 -0400
@@ -98,6 +98,6 @@
 ## Total Length: 14220
 ## Total NonMask ( excluding >20bp runs of N/X bases ): 14220
 ## Total NonSub ( excluding all non ACGT bases ):14220
-RepeatMasker version open-4.0.7 , default mode
-run with rmblastn version 2.2.27+
-RepeatMasker Combined Database: Dfam_Consensus-20170127
+RepeatMasker version open-4.0.9 , default mode
+run with rmblastn version 2.9.0+
+RepeatMasker Combined Database: Dfam-Dfam_3.0
diff -r ade773848c3d -r 438f65cb1d14 test-data/small.fasta.gff
--- a/test-data/small.fasta.gff	Thu Jan 23 04:40:29 2020 -0500
+++ b/test-data/small.fasta.gff	Tue Aug 18 05:39:55 2020 -0400
@@ -1,6 +1,6 @@
 ##gff-version 2
-##date 2018-04-21
-##sequence-region dataset_12.dat
+##date 2020-08-18
+##sequence-region rm_input.fasta
 scaffold_1	RepeatMasker	similarity	613	632	 0.0	+	.	Target "Motif:(GT)n" 1 20
 scaffold_1	RepeatMasker	similarity	780	824	18.3	+	.	Target "Motif:(ATAATA)n" 1 45
 scaffold_1	RepeatMasker	similarity	2231	2274	23.9	+	.	Target "Motif:(CAGA)n" 1 46
diff -r ade773848c3d -r 438f65cb1d14 test-data/small.fasta.stats
--- a/test-data/small.fasta.stats	Thu Jan 23 04:40:29 2020 -0500
+++ b/test-data/small.fasta.stats	Tue Aug 18 05:39:55 2020 -0400
@@ -1,5 +1,5 @@
 ==================================================
-file name: dataset_12.dat           
+file name: rm_input.fasta           
 sequences:             1
 total length:      14220 bp  (14220 bp excl N/X-runs) 
 GC level:         39.94 %
@@ -45,8 +45,8 @@
 
 
 The query species was assumed to be homo          
-RepeatMasker Combined Database: Dfam_Consensus-20170127
-                          
-run with rmblastn version 2.2.27+
-The query was compared to unclassified sequences in ".../dataset_2.dat"
+RepeatMasker Combined Database: Dfam-Dfam_3.0
+                                    
+run with rmblastn version 2.9.0+
+The query was compared to unclassified sequences in ".../dataset_257a7a8f-7065-486a-ae21-53e1fceff0f8.dat"
 
diff -r ade773848c3d -r 438f65cb1d14 test-data/small_repbase.fasta.stats
--- a/test-data/small_repbase.fasta.stats	Thu Jan 23 04:40:29 2020 -0500
+++ b/test-data/small_repbase.fasta.stats	Tue Aug 18 05:39:55 2020 -0400
@@ -54,7 +54,7 @@
 
 
 The query species was assumed to be anopheles genus
-RepeatMasker Combined Database: Dfam_Consensus-20170127
-                          
-run with rmblastn version 2.2.27+
+RepeatMasker Combined Database: Dfam-Dfam_3.0
+                                    
+run with rmblastn version 2.9.0+