# HG changeset patch # User iuc # Date 1473886547 14400 # Node ID f7094efef9032c6e6344665f8917118e9240d61d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db diff -r 000000000000 -r f7094efef903 bwameth.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bwameth.xml Wed Sep 14 16:55:47 2016 -0400 @@ -0,0 +1,118 @@ + + 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 000000000000 -r f7094efef903 test-data/output.bam Binary file test-data/output.bam has changed diff -r 000000000000 -r f7094efef903 test-data/ref.fa.gz Binary file test-data/ref.fa.gz has changed diff -r 000000000000 -r f7094efef903 test-data/t_R1.fastq.gz Binary file test-data/t_R1.fastq.gz has changed diff -r 000000000000 -r f7094efef903 test-data/t_R2.fastq.gz Binary file test-data/t_R2.fastq.gz has changed diff -r 000000000000 -r f7094efef903 tool-data/bwameth_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/bwameth_indexes.loc.sample Wed Sep 14 16:55:47 2016 -0400 @@ -0,0 +1,10 @@ +# 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 diff -r 000000000000 -r f7094efef903 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Sep 14 16:55:47 2016 -0400 @@ -0,0 +1,6 @@ + + + value, name, path + +
+
diff -r 000000000000 -r f7094efef903 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Sep 14 16:55:47 2016 -0400 @@ -0,0 +1,9 @@ + + + + + + + + +