# HG changeset patch
# User iuc
# Date 1468435672 14400
# Node ID ee804c6f3b97ebdca04fdcb936b30ff3464d5850

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7

diff -r 000000000000 -r ee804c6f3b97 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Jul 13 14:47:52 2016 -0400
@@ -0,0 +1,28 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="stringtie" version="1.2.3">
+      <install version="1.0">
+            <actions>
+                <action type="download_by_url" sha256sum="1a323fd17c24889748c645b3dfe5a06305236d9899e87a27939a68404d2d9d09">https://ccb.jhu.edu/software/stringtie/dl/stringtie-1.2.3.tar.gz</action>
+                <action type="shell_command">make release</action>
+                <action type="move_file">
+                    <source>stringtie</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="set_to" name="STRINGTIE_ROOT_PATH">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
+It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and
+quantitate full-length transcripts representing multiple splice variants for each gene locus.
+Its input can include not only the alignments of raw reads used by other transcript assemblers,
+but also alignments longer sequences that have been assembled from those reads.
+To identify differentially expressed genes between experiments, StringTie's
+output can be processed either by the Cuffdiff or Ballgown programs.
+        </readme>
+    </package>
+</tool_dependency>