Mercurial > repos > bernhardlutz > rnabob
changeset 0:ffb3e57089ee draft
Uploaded
author | bernhardlutz |
---|---|
date | Tue, 20 May 2014 14:44:25 -0400 |
parents | |
children | cc8ae959f7b5 |
files | rnabob.xml tool_dependencies.xml |
diffstat | 2 files changed, 57 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /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>
--- /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>