Mercurial > repos > bgruening > repeat_masker

changeset 12:07acb3a096d7 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker commit 7a5f368a5859e659aa36d0358bb96ca12574e2cc
author iuc
date Mon, 24 Apr 2023 10:40:41 +0000
parents fa311361317b
children
files macros.xml test-data/Dfam_partial_test.h5 test-data/README.md test-data/small.fasta.cat test-data/small.fasta.gff test-data/small.fasta.log test-data/small.fasta.stats test-data/small_dfam.fasta.cat test-data/small_dfam.fasta.log test-data/small_dfam.fasta.stats test-data/small_dfam_rattus.fasta.cat test-data/small_dfam_rattus.fasta.log test-data/small_dfam_rattus.fasta.stats test-data/small_dfam_up.fasta.cat test-data/small_dfam_up.fasta.log test-data/small_dfam_up.fasta.stats
diffstat 16 files changed, 52 insertions(+), 47 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu Oct 21 15:48:56 2021 +0000
+++ b/macros.xml	Mon Apr 24 10:40:41 2023 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">4.1.2-p1</token>
-    <token name="@VERSION_SUFFIX@">galaxy1</token>
+    <token name="@TOOL_VERSION@">4.1.5</token>
+    <token name="@VERSION_SUFFIX@">galaxy0</token>
     <xml name="edam_ontology">
         <edam_topics>
             <edam_topic>topic_0157</edam_topic>
Binary file test-data/Dfam_partial_test.h5 has changed
--- a/test-data/README.md	Thu Oct 21 15:48:56 2021 +0000
+++ b/test-data/README.md	Mon Apr 24 10:40:41 2023 +0000
@@ -1,1 +1,4 @@
-Dfam_partial_test.h5 was generated from the test dataset in https://github.com/Dfam-consortium/FamDB/ (commit: 6b28b66)
+Dfam_partial_test.h5 was generated from the test dataset in https://github.com/Dfam-consortium/FamDB/ (commit: 20c436d)
+
+`./export_dfam.py --from-tax-dump /path/to/taxonomy_dump/from_ncbi/ --from-hmm test_data/Dfam_partial.hmm --db-version 1.0 Dfam_partial_test.h5`
+
--- a/test-data/small.fasta.cat	Thu Oct 21 15:48:56 2021 +0000
+++ b/test-data/small.fasta.cat	Mon Apr 24 10:40:41 2023 +0000
@@ -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 4.1.2-p1 , default mode
-run with rmblastn version 2.10.0+
+RepeatMasker version 4.1.5 , default mode
+run with rmblastn version 2.13.0+
 RM Library: 
--- a/test-data/small.fasta.gff	Thu Oct 21 15:48:56 2021 +0000
+++ b/test-data/small.fasta.gff	Mon Apr 24 10:40:41 2023 +0000
@@ -1,11 +1,10 @@
-##gff-version 2
-##date 2021-05-20
-##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
-scaffold_1	RepeatMasker	similarity	4853	4901	18.4	+	.	Target "Motif:(TC)n" 1 54
-scaffold_1	RepeatMasker	similarity	6230	6284	19.1	+	.	Target "Motif:(TAATTAA)n" 1 52
-scaffold_1	RepeatMasker	similarity	6548	6606	28.3	+	.	Target "Motif:(GACA)n" 1 57
-scaffold_1	RepeatMasker	similarity	11981	12050	 2.9	+	.	Target "Motif:(CT)n" 1 71
-scaffold_1	RepeatMasker	similarity	12078	12113	15.4	+	.	Target "Motif:(CT)n" 1 37
+##gff-version 3
+##sequence-region scaffold_1 1 14220
+scaffold_1	RepeatMasker	dispersed_repeat	613	632	 0.0	+	.	ID=1;Target "Motif:(GT)n" 1 20
+scaffold_1	RepeatMasker	dispersed_repeat	780	824	18.3	+	.	ID=2;Target "Motif:(ATAATA)n" 1 45
+scaffold_1	RepeatMasker	dispersed_repeat	2231	2274	23.9	+	.	ID=3;Target "Motif:(CAGA)n" 1 46
+scaffold_1	RepeatMasker	dispersed_repeat	4853	4901	18.4	+	.	ID=4;Target "Motif:(TC)n" 1 54
+scaffold_1	RepeatMasker	dispersed_repeat	6230	6284	19.1	+	.	ID=5;Target "Motif:(TAATTAA)n" 1 52
+scaffold_1	RepeatMasker	dispersed_repeat	6548	6606	28.3	+	.	ID=6;Target "Motif:(GACA)n" 1 57
+scaffold_1	RepeatMasker	dispersed_repeat	11981	12050	 2.9	+	.	ID=7;Target "Motif:(CT)n" 1 71
+scaffold_1	RepeatMasker	dispersed_repeat	12078	12113	15.4	+	.	ID=8;Target "Motif:(CT)n" 1 37
--- a/test-data/small.fasta.log	Thu Oct 21 15:48:56 2021 +0000
+++ b/test-data/small.fasta.log	Mon Apr 24 10:40:41 2023 +0000
@@ -1,4 +1,4 @@
-SW scoret% div.t% del.t% ins.tquery sequencetpos in  query: begintendt(left)trepeattclass/familytpos in repeat: begintendt(left)tID
+SW score	% div.	% del.	% ins.	query sequence	pos in  query: begin	end	(left)	repeat	class/family	pos in repeat: begin	end	(left)	ID
 
 18	0.0	0.0	0.0	scaffold_1	613	632	(13588)	(GT)n	Simple_repeat	1	20	(0)	1
 16	18.3	2.2	2.2	scaffold_1	780	824	(13396)	(ATAATA)n	Simple_repeat	1	45	(0)	2
--- a/test-data/small.fasta.stats	Thu Oct 21 15:48:56 2021 +0000
+++ b/test-data/small.fasta.stats	Mon Apr 24 10:40:41 2023 +0000
@@ -10,7 +10,7 @@
 --------------------------------------------------
 Retroelements            0            0 bp    0.00 %
    SINEs:                0            0 bp    0.00 %
-   Penelope              0            0 bp    0.00 %
+   Penelope:             0            0 bp    0.00 %
    LINEs:                0            0 bp    0.00 %
     CRE/SLACS            0            0 bp    0.00 %
      L2/CR1/Rex          0            0 bp    0.00 %
@@ -28,7 +28,7 @@
    hobo-Activator        0            0 bp    0.00 %
    Tc1-IS630-Pogo        0            0 bp    0.00 %
    En-Spm                0            0 bp    0.00 %
-   MuDR-IS905            0            0 bp    0.00 %
+   MULE-MuDR             0            0 bp    0.00 %
    PiggyBac              0            0 bp    0.00 %
    Tourist/Harbinger     0            0 bp    0.00 %
    Other (Mirage,        0            0 bp    0.00 %
@@ -53,8 +53,8 @@
   Runs of >=20 X/Ns in query were excluded in % calcs
 
 
-RepeatMasker version 4.1.2-p1 , default mode
-                                     
-run with rmblastn version 2.10.0+
-The query was compared to unclassified sequences in ".../dataset_a3b3078d-de09-4651-9e83-62019a3d45ba.dat"
+RepeatMasker version 4.1.5 , default mode
+                                        
+run with rmblastn version 2.13.0+
+The query was compared to unclassified sequences in ".../dataset_9e3ddbd2-0776-4c6d-bed6-0f4cd415796c.dat"
 FamDB: 
--- a/test-data/small_dfam.fasta.cat	Thu Oct 21 15:48:56 2021 +0000
+++ b/test-data/small_dfam.fasta.cat	Mon Apr 24 10:40:41 2023 +0000
@@ -82,6 +82,7 @@
 
 Matrix = 25p39g.matrix
 Kimura (with divCpGMod) = 29.45
+CpG sites = 10, Kimura (unadjusted) = 31.65
 Transitions / transversions = 1.43 (10/7)
 Gap_init rate = 0.07 (5 / 70), avg. gap size = 1.00 (5 / 5)
 
@@ -113,6 +114,6 @@
 ## Total Length: 14220
 ## Total NonMask ( excluding >20bp runs of N/X bases ): 14220
 ## Total NonSub ( excluding all non ACGT bases ):14220
-RepeatMasker version 4.1.2-p1 , default mode
-run with rmblastn version 2.10.0+
-RM Library: CONS-Dfam_3.3
+RepeatMasker version 4.1.5 , default mode
+run with rmblastn version 2.13.0+
+RM Library: CONS-Dfam_3.7
--- a/test-data/small_dfam.fasta.log	Thu Oct 21 15:48:56 2021 +0000
+++ b/test-data/small_dfam.fasta.log	Mon Apr 24 10:40:41 2023 +0000
@@ -1,4 +1,4 @@
-SW scoret% div.t% del.t% ins.tquery sequencetpos in  query: begintendt(left)trepeattclass/familytpos in repeat: begintendt(left)tID
+SW score	% div.	% del.	% ins.	query sequence	pos in  query: begin	end	(left)	repeat	class/family	pos in repeat: begin	end	(left)	ID
 
 18	0.0	0.0	0.0	scaffold_1	613	632	(13588)	(GT)n	Simple_repeat	1	20	(0)	1
 16	18.3	2.2	2.2	scaffold_1	780	824	(13396)	(ATAATA)n	Simple_repeat	1	45	(0)	2
--- a/test-data/small_dfam.fasta.stats	Thu Oct 21 15:48:56 2021 +0000
+++ b/test-data/small_dfam.fasta.stats	Mon Apr 24 10:40:41 2023 +0000
@@ -45,7 +45,7 @@
 
 
 The query species was assumed to be human         
-RepeatMasker version 4.1.2-p1 , default mode
-                                     
-run with rmblastn version 2.10.0+
-FamDB: CONS-Dfam_3.3
+RepeatMasker version 4.1.5 , default mode
+                                        
+run with rmblastn version 2.13.0+
+FamDB: CONS-Dfam_3.7
--- a/test-data/small_dfam_rattus.fasta.cat	Thu Oct 21 15:48:56 2021 +0000
+++ b/test-data/small_dfam_rattus.fasta.cat	Mon Apr 24 10:40:41 2023 +0000
@@ -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 4.1.2-p1 , default mode
-run with rmblastn version 2.10.0+
-RM Library: CONS-Dfam_3.3
+RepeatMasker version 4.1.5 , default mode
+run with rmblastn version 2.13.0+
+RM Library: CONS-Dfam_3.7
--- a/test-data/small_dfam_rattus.fasta.log	Thu Oct 21 15:48:56 2021 +0000
+++ b/test-data/small_dfam_rattus.fasta.log	Mon Apr 24 10:40:41 2023 +0000
@@ -1,4 +1,4 @@
-SW scoret% div.t% del.t% ins.tquery sequencetpos in  query: begintendt(left)trepeattclass/familytpos in repeat: begintendt(left)tID
+SW score	% div.	% del.	% ins.	query sequence	pos in  query: begin	end	(left)	repeat	class/family	pos in repeat: begin	end	(left)	ID
 
 18	0.0	0.0	0.0	scaffold_1	613	632	(13588)	(GT)n	Simple_repeat	1	20	(0)	1
 16	18.3	2.2	2.2	scaffold_1	780	824	(13396)	(ATAATA)n	Simple_repeat	1	45	(0)	2
--- a/test-data/small_dfam_rattus.fasta.stats	Thu Oct 21 15:48:56 2021 +0000
+++ b/test-data/small_dfam_rattus.fasta.stats	Mon Apr 24 10:40:41 2023 +0000
@@ -14,6 +14,7 @@
       IDs              0            0 bp    0.00 %
       MIRs             0            0 bp    0.00 %
 
+
 LINEs:                 0            0 bp    0.00 %
       LINE1            0            0 bp    0.00 %
       LINE2            0            0 bp    0.00 %
@@ -47,7 +48,7 @@
 
 
 The query species was assumed to be rattus        
-RepeatMasker version 4.1.2-p1 , default mode
-                                     
-run with rmblastn version 2.10.0+
-FamDB: CONS-Dfam_3.3
+RepeatMasker version 4.1.5 , default mode
+                                        
+run with rmblastn version 2.13.0+
+FamDB: CONS-Dfam_3.7
--- a/test-data/small_dfam_up.fasta.cat	Thu Oct 21 15:48:56 2021 +0000
+++ b/test-data/small_dfam_up.fasta.cat	Mon Apr 24 10:40:41 2023 +0000
@@ -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 4.1.2-p1 , default mode
-run with rmblastn version 2.10.0+
-RM Library: CONS-_
+RepeatMasker version 4.1.5 , default mode
+run with rmblastn version 2.13.0+
+RM Library: CONS-Dfam_1.0
--- a/test-data/small_dfam_up.fasta.log	Thu Oct 21 15:48:56 2021 +0000
+++ b/test-data/small_dfam_up.fasta.log	Mon Apr 24 10:40:41 2023 +0000
@@ -1,4 +1,4 @@
-SW scoret% div.t% del.t% ins.tquery sequencetpos in  query: begintendt(left)trepeattclass/familytpos in repeat: begintendt(left)tID
+SW score	% div.	% del.	% ins.	query sequence	pos in  query: begin	end	(left)	repeat	class/family	pos in repeat: begin	end	(left)	ID
 
 18	0.0	0.0	0.0	scaffold_1	613	632	(13588)	(GT)n	Simple_repeat	1	20	(0)	1
 16	18.3	2.2	2.2	scaffold_1	780	824	(13396)	(ATAATA)n	Simple_repeat	1	45	(0)	2
--- a/test-data/small_dfam_up.fasta.stats	Thu Oct 21 15:48:56 2021 +0000
+++ b/test-data/small_dfam_up.fasta.stats	Mon Apr 24 10:40:41 2023 +0000
@@ -14,6 +14,7 @@
       IDs              0            0 bp    0.00 %
       MIRs             0            0 bp    0.00 %
 
+
 LINEs:                 0            0 bp    0.00 %
       LINE1            0            0 bp    0.00 %
       LINE2            0            0 bp    0.00 %
@@ -47,7 +48,7 @@
 
 
 The query species was assumed to be rodent        
-RepeatMasker version 4.1.2-p1 , default mode
-                                     
-run with rmblastn version 2.10.0+
-FamDB: CONS-_
+RepeatMasker version 4.1.5 , default mode
+                                        
+run with rmblastn version 2.13.0+
+FamDB: CONS-Dfam_1.0