# HG changeset patch
# User dpryan79
# Date 1473929832 14400
# Node ID 5924e53ef39c0c16ebc925d12bffe0712fe01f06
# Parent 54c3b261783b40d574b8747a263dad57da1226e6
Uploaded
diff -r 54c3b261783b -r 5924e53ef39c .shed.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml Thu Sep 15 04:57:12 2016 -0400
@@ -0,0 +1,14 @@
+categories:
+- Sequence Analysis
+- Next Gen Mappers
+description: Fast and accurate alignment of BS-seq reads.
+long_description: |
+ A fast and accurate aligner of BS-seq data.
+
+ - Supports single-end and paired-end alignments
+ - Supports gapped alignments
+ - Faster and more sensitive than many other tools
+name: bwameth
+owner: iuc
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tools/bwameth
+type: unrestricted
diff -r 54c3b261783b -r 5924e53ef39c bwameth.xml
--- a/bwameth.xml Wed Sep 14 07:54:59 2016 -0400
+++ b/bwameth.xml Thu Sep 15 04:57:12 2016 -0400
@@ -1,20 +1,11 @@
-
- Fast and accurate aligner of BS-Seq reads.
-
- toolshed
- samtools
- bwa
- bwameth
-
-
-
-
-
-
-
-
- bwameth.py --version
-
+
+ Fast and accurate aligner of BS-Seq reads.
+
+ samtools
+ bwameth
+
+ bwameth.py --version
+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
+
+
+ @misc{1401.1129,
+ Author = {Brent S. Pedersen and Kenneth Eyring and Subhajyoti De and Ivana V. Yang and David A. Schwartz},
+ Title = {Fast and accurate alignment of long bisulfite-seq reads},
+ Year = {2014},
+ Eprint = {arXiv:1401.1129},
+ }
+
diff -r 54c3b261783b -r 5924e53ef39c test-data/output.bam
Binary file test-data/output.bam has changed
diff -r 54c3b261783b -r 5924e53ef39c test-data/ref.fa.gz
Binary file test-data/ref.fa.gz has changed
diff -r 54c3b261783b -r 5924e53ef39c test-data/t_R1.fastq.gz
Binary file test-data/t_R1.fastq.gz has changed
diff -r 54c3b261783b -r 5924e53ef39c test-data/t_R2.fastq.gz
Binary file test-data/t_R2.fastq.gz has changed
diff -r 54c3b261783b -r 5924e53ef39c tool-data/bwameth_indexes.loc.sample
--- a/tool-data/bwameth_indexes.loc.sample Wed Sep 14 07:54:59 2016 -0400
+++ b/tool-data/bwameth_indexes.loc.sample Thu Sep 15 04:57:12 2016 -0400
@@ -1,10 +1,15 @@
# This is a sample file distributed with Galaxy that is used to define a
# list of bwa-meth indices, using three columns tab separated:
#
-# bwameth_index_id\tSome description text\t/path/to/genome.fasta
+#
#
# An index can be created with the following command:
#
# bwameth.py index /some/path/genome.fa
#
# "/some/path/genome.fa" would then be the last column in the line
+# If this were for the mm10 mouse genome, the resulting entry would look like:
+#
+#mm9 mm9 Mouse (mm9) /some/path/genome.fa
+#
+#
diff -r 54c3b261783b -r 5924e53ef39c tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample Wed Sep 14 07:54:59 2016 -0400
+++ b/tool_data_table_conf.xml.sample Thu Sep 15 04:57:12 2016 -0400
@@ -1,6 +1,6 @@
- value, name, path
+ value, dbkey, name, path
diff -r 54c3b261783b -r 5924e53ef39c tool_dependencies.xml
--- a/tool_dependencies.xml Wed Sep 14 07:54:59 2016 -0400
+++ b/tool_dependencies.xml Thu Sep 15 04:57:12 2016 -0400
@@ -1,12 +1,9 @@
-
-
-
-
-
+
+