# HG changeset patch
# User rnateam
# Date 1450390208 18000
# Node ID 0d988a56e3320809d3880465320204dba11f7a51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/metilene commit 090bc9bb5c775600f4727d8729a032b52e78bd05-dirty
diff -r 000000000000 -r 0d988a56e332 metilene.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/metilene.xml Thu Dec 17 17:10:08 2015 -0500
@@ -0,0 +1,127 @@
+
+
+
+ calling differentially methylated regions from bisulfite sequencing data
+
+
+ metilene
+ perl
+ R
+ r_ggplot2
+ bedtools
+ gnu_coreutils
+
+
+
+
+
+ echo "0.2-4"
+ /dev/null 2>/dev/null
+ &&
+ ## metilene main program
+ metilene
+ -M $Options.opt_M
+ -m $Options.opt_m
+ -d $Options.opt_d
+ -t 1
+ -f 1
+ -v $Options.opt_v
+ metilene_g1_g2.input
+ >$output_bedlike
+ 2>/dev/null
+ &&
+ ## postprocessing
+ cut -f1-4 $output_bedlike > $output_bedgraph 2>/dev/null
+ &&
+ ## write to job directory
+ metilene_output.pl
+ -q $output_bedlike
+ -p 0.05
+ -o ./metilene >/dev/null 2>/dev/null
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ @Article{Juhling_Kretzmer_Bernhart-metil_Fast_and-2015,
+ author = {Juhling, Frank and Kretzmer, Helene and Bernhart, Stephan
+ H. and Otto, Christian and Stadler, Peter F. and Hoffmann,
+ Steve},
+ title = {metilene: {Fast} and sensitive calling of differentially
+ methylated regions from bisulfite sequencing data},
+ page = {[Epub ahead of print]},
+ journal = {Genome Res},
+ year = {2015},
+ pmid = {26631489},
+ doi = {10.1101/gr.196394.115},
+ issn = {1088-9051},
+ issn = {1549-5469}}
+
+
diff -r 000000000000 -r 0d988a56e332 test-data/example_S1.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example_S1.bedgraph Thu Dec 17 17:10:08 2015 -0500
@@ -0,0 +1,10699 @@
+#chrom start end S1
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diff -r 000000000000 -r 0d988a56e332 test-data/example_S2.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example_S2.bedgraph Thu Dec 17 17:10:08 2015 -0500
@@ -0,0 +1,10699 @@
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diff -r 000000000000 -r 0d988a56e332 test-data/example_S3.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example_S3.bedgraph Thu Dec 17 17:10:08 2015 -0500
@@ -0,0 +1,10699 @@
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diff -r 000000000000 -r 0d988a56e332 test-data/example_S4.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example_S4.bedgraph Thu Dec 17 17:10:08 2015 -0500
@@ -0,0 +1,10699 @@
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diff -r 000000000000 -r 0d988a56e332 test-data/example_S5.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example_S5.bedgraph Thu Dec 17 17:10:08 2015 -0500
@@ -0,0 +1,10699 @@
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diff -r 000000000000 -r 0d988a56e332 test-data/example_S6.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example_S6.bedgraph Thu Dec 17 17:10:08 2015 -0500
@@ -0,0 +1,10699 @@
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diff -r 000000000000 -r 0d988a56e332 test-data/example_S7.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example_S7.bedgraph Thu Dec 17 17:10:08 2015 -0500
@@ -0,0 +1,10699 @@
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diff -r 000000000000 -r 0d988a56e332 test-data/example_S8.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example_S8.bedgraph Thu Dec 17 17:10:08 2015 -0500
@@ -0,0 +1,10699 @@
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diff -r 000000000000 -r 0d988a56e332 test-data/metilene.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/metilene.out Thu Dec 17 17:10:08 2015 -0500
@@ -0,0 +1,102 @@
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diff -r 000000000000 -r 0d988a56e332 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Thu Dec 17 17:10:08 2015 -0500
@@ -0,0 +1,50 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ https://depot.galaxyproject.org/software/metilene/metilene_0.2-4_src_all.tar.gz
+
+ make
+
+
+ metilene
+ $INSTALL_DIR/bin
+
+
+ metilene_input.pl
+ $INSTALL_DIR/bin
+
+
+ metilene_output.pl
+ $INSTALL_DIR/bin
+
+
+ metilene_output.R
+ $INSTALL_DIR/bin
+
+
+
+ $INSTALL_DIR/bin
+
+
+
+ Metilene is precompiled for Linux
+
+