# HG changeset patch
# User bgruening
# Date 1405150127 14400
# Node ID 2306a9c40c3770a4161d682d06c69195febf5538
Uploaded
diff -r 000000000000 -r 2306a9c40c37 README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Sat Jul 12 03:28:47 2014 -0400
@@ -0,0 +1,53 @@
+Galaxy wrappers for sailfish
+=====================================
+
+These wrappers are copyright 2014 by Björn Grüning and additional contributors.
+All rights reserved. See the licence text below.
+
+Currently tested with sailfish 0.6.3.
+
+
+Automated Installation
+======================
+
+Galaxy should be able to automatically install the sailfish for you.
+
+
+History
+=======
+
+======== ======================================================================
+Version Changes
+-------- ----------------------------------------------------------------------
+v0.6.3.0 - First release
+
+======== ======================================================================
+
+
+Bug Reports
+===========
+
+You can file an issue here https://github.com/bgruening/galaxytools/issues or ask
+us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev
+
+
+Licence (MIT)
+=============
+
+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 2306a9c40c37 sailfish.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/sailfish.xml Sat Jul 12 03:28:47 2014 -0400
@@ -0,0 +1,81 @@
+
+ transcript quantification from RNA-seq data
+ sailfish -version
+
+
+>"
+ #elif $single_or_paired_opts.orientation == "away":
+ -l "TYPE=PE:O=<>"
+ #else:
+ -l "TYPE=PE:O=><"
+ #end if
+ #end if
+-o
+
+]]>
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+> denotes that the mates are oriented in the same direction --- e.g. if the 5' end of mate 1 is
+upstream from the 3' end, then the 5' end of mate 2 is upstream from its 3' end and vice-versa.
+
+The second option <> denotes that the mates are oriented away from each other. This implies that start
+of mate1 is closer to start of mate 2 than the end of mate 2, etc.
+
+The third option >< is, perhaps, the most common relative orientation. It denotes that the mates are
+oriented toward each other, so that the start of mate 1 is farther from the start of mate 2 than it is from the end of mate 2 and vice-versa.
+
+-------
+
+**References**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following:
+
+
+]]>
+
+
diff -r 000000000000 -r 2306a9c40c37 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Sat Jul 12 03:28:47 2014 -0400
@@ -0,0 +1,6 @@
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