# HG changeset patch
# User yating-l
# Date 1486505091 18000
# Node ID 25175ee4eb90e5f9605185ab01f2ca85ebe34a56
planemo upload commit 54155cb43a07d563ee6861c2410a167b9c879ff4-dirty
diff -r 000000000000 -r 25175ee4eb90 LICENSE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE Tue Feb 07 17:04:51 2017 -0500
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+The MIT License (MIT)
+
+Copyright (c) 2016 Rémi Marenco
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff -r 000000000000 -r 25175ee4eb90 README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Tue Feb 07 17:04:51 2017 -0500
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+# bamToBigwig
+Galaxy wrapper for Bam to Bigwig conversion
diff -r 000000000000 -r 25175ee4eb90 bam_to_bigwig.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bam_to_bigwig.xml Tue Feb 07 17:04:51 2017 -0500
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+
+
+ ucsc_tools
+ bedtools
+
+
+
+
+ chrom.sizes;
+ bedtools genomecov -bg -split -ibam $input_bam -g chrom.sizes > temp.bg;
+ bedGraphToBigWig temp.bg chrom.sizes $output_bigwig;
+ ]]>
+
+
+
+
+
+
+
+
+ This tool converts a Bam file to a BigWig file.
+
+ It needs:
+ - A Bam file
+ - The reference genome as a Fasta file
+
+
\ No newline at end of file
diff -r 000000000000 -r 25175ee4eb90 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue Feb 07 17:04:51 2017 -0500
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+
+
+
+
+
+
+ http://old-gep.wustl.edu/~galaxy/ucsc_tools_340.tar.gz
+
+ .
+ $INSTALL_DIR/bin
+
+
+
+ $INSTALL_DIR/bin
+
+
+
+ The well known UCSC tools from Jim Kent.
+
+
+
+
+
+
+