# HG changeset patch
# User bernhardlutz
# Date 1400611465 14400
# Node ID ffb3e57089ee2955cb1e7298563fcb5f602254c6

Uploaded

diff -r 000000000000 -r ffb3e57089ee rnabob.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnabob.xml	Tue May 20 14:44:25 2014 -0400
@@ -0,0 +1,39 @@
+<tool id="rnabob" name="RNABob" version="2.2.1">
+    <description>Fast Pattern searching for RNA secondary structures</description>
+    <requirements>
+        <requirement type="package" version="2.2.1">rnabob</requirement>
+    </requirements>
+    <command>
+rnabob 
+$descriptor_file
+$sequence_file
+$search
+$skip_mode
+$fancy
+$quiet
+> $outfile
+    </command>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
+        <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
+    </stdio>
+    <inputs>
+        <param format="txt" name="descriptor_file" type="file" label="Descriptor File" help="" />
+        <param format="txt" name="sequence_file" type="file" label="Sequence File" help="" />
+        <param name="search" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Search both strands of database" help="" />
+        <param name="skip_mode" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Skip Mode: Disallow overlapping matches" help="" />
+        <param name="fancy" type="boolean" checked="false" truevalue="-F" falsevalue="" label="Fancy: Show full alignments to pattern" help="" />
+        <param name="quiet" type="boolean" checked="false" truevalue="-q" falsevalue="" label="Quiet: Suppress verbose banner and headers" help="" />
+    </inputs>
+    <outputs>
+        <data name="outfile" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>**What it does**
+    http://selab.janelia.org/software.html
+    
+RNABOB is an implementation of D. Gautheret's RNAMOT, but with a different underlying algorithm using a nondeterministic finite state machine with node rewriting rules. (Computer scientists would probably cringe in horror. It works, and it's fast, but is it street legal in a computer science department? Who knows.) An RNABOB motif is a consensus pattern a la PROSITE patterns, but with base-pairing. 
+
+    </help>
+</tool>
diff -r 000000000000 -r ffb3e57089ee tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue May 20 14:44:25 2014 -0400
@@ -0,0 +1,18 @@
+<tool_dependency>
+    <package name="rnabob" version="2.2.1">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://selab.janelia.org/software/rnabob/rnabob.tar.gz</action>
+                <action type="shell_command">make</action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+                <action type="move_file">
+                    <source>rnabob</source>
+                    <destination>$INSTALL_DIR</destination>
+                </action>
+            </actions>
+        </install>
+        <readme>Compiling rnabob requires a C compiler (typically gcc)</readme>
+    </package>
+</tool_dependency>