diff rnabob.xml @ 0:cd00b4fe6552 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnabob.xml	Mon Dec 22 09:08:31 2014 -0500
@@ -0,0 +1,218 @@
+<tool id="rbc_rnabob" name="RNABOB" version="2.2.1.0">
+    <description>Fast Pattern searching for RNA secondary structures</description>
+    <requirements>
+        <requirement type="package" version="2.2.1">rnabob</requirement>
+    </requirements>
+    <version_command>echo "2.2.1"</version_command>
+    <command>
+<![CDATA[
+    rnabob 
+    	-q
+    	$fancy
+    	$compStrands
+    	$skipOverlapping
+    	$descriptorFile
+    	$sequenceFile > $stdout
+]]>
+    </command>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
+        <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
+    </stdio>
+    <inputs>
+        <param name="descriptorFile" type="data" format="txt" multiple="false" label="Motif Descriptor File" help="This file contains the description of the motif for which to search"/>
+	    <param name="sequenceFile" type="data" format="fasta" multiple="false" label="Sequence File" help="This file specifies the sequence in which the motif will be searched"/>
+	    <param name="compStrands" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Also search on complementary strands" help="-c : Search both strands of the supplied sequence"/>
+	    <param name="skipOverlapping" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Skip overlapping matches" help="-s : This is a workaround to avoid a problem in the DNABANK, overlapping matches will be ignored"/>
+	    <param name="fancy" type="boolean" checked="false" truevalue="-F" falsevalue="" label="Show Alignments" help="Display full alignments to pattern"/>
+    </inputs>
+    <outputs>
+        <data format="txt" name="stdout" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="descriptorFile" value="r17.des" />
+            <param name="sequenceFile" value="F22B7.fa" />
+            <param name="compStrands" value="True" />
+            <param name="skipOverlapping" value="False" />
+            <param name="fancy" value="False" />
+            <output name="stdout" file="r17.bob" />
+        </test>
+        <test>
+            <param name="descriptorFile" value="trna.des" />
+            <param name="sequenceFile" value="F22B7.fa" />
+            <param name="compStrands" value="True" />
+            <param name="skipOverlapping" value="False" />
+            <param name="fancy" value="False" />
+            <output name="stdout" file="trna.bob" />
+        </test>
+    </tests>
+    <help>
+**What RNABOB does**
+
+RNABOB allows searching a sequence database for RNA structural motifs.
+The probe motif is specified in a *descriptor* file,
+which describes its primary sequence, secondary structure, and tertiary constraints.
+The source in its original packaging can be found at http://selab.janelia.org/software/#rnabob.
+
+-----
+
+**Sequence database format**
+
+RNABOB is currently restricted to reading sequence files in FASTA format. 
+The command line version of RNABOB can also read sequence files in GCG, EMBL, GenBank and other formats.
+
+-----
+
+**Descriptor file syntax**
+
+The descriptor file syntax is fairly powerful, and allows a great deal of freedom for specifying 
+RNA motifs. The syntax is therefore a bit complicated.
+
+The descriptor file has two parts: a **topology** description and an **explicit** description.
+
+The first non-blank, non-comment line of the file is the topology description. It defines the 
+order of occurrence of a series of single-stranded, double-stranded and related elements. Each 
+element must be given a unique name (a number, typically) and must be prefixed with '**s**', 
+'**h**', or '**r**', indicating single-strand, helical, or a relational element. Helical and 
+relational elements are paired to other elements, which are suffixed by a prime, **\'**.
+
+For example::
+
+	\
+			h1 s1 h1'
+
+describes a hairpin loop structure with a simple helix and single-stranded loop. If the helix 
+always contained a non-canonical base pair at one position, the topology coud be described as::
+
+	\
+			h1 r1 h2 s1 h2' r1' h1'
+
+where r1,r1' indicate a correlation, where the sequence r1 constrains the sequence of r1'. 
+(Helices are a special case of this.)
+
+The remaining non-comment, non-blank lines are explicit descriptions of each element in turn. Each 
+line contains 3 or 4 fields, separated by tabs or blank space. The first field is the name of the 
+element, from the topology description. The second field is the number of mismatches allowed in 
+this element. The third field is the primary sequence constraint to apply to this element.
+
+Helices and relational element pairs are specified on a single line rather than two. Mismatches 
+and primary sequence constraints are given as pairs, separated by a colon '**:**'. The left side 
+is the constraint applied to the upstream element, and the right side is applied to the downstream 
+elements.
+
+The primary sequence constraint is given as a sequence of nucleotides. Any IUPAC single-letter 
+code is recognized, including N if the position can have any base identity. Allowed length 
+variations are specified with asterisks ``'*'``, where each ``*`` will allow either 0 or 1 N at 
+that position.
+
+For example::
+
+	\
+			GGAGG******NNNAUG
+
+specifies a GGAGG Shine/Dalgarno site and an AUG initiation codon, separated by a spacer of 3 to 9 
+nucleotides of any sequence.
+
+An alternative syntax can be used for very long gaps::
+
+	\
+			GGAGG[10]NNNAUG is the same as GGAGG**********NNNAUG
+
+Be careful defining variable length helices and relational elements; if the number and type (gap 
+or identity) of position do not match on left and right sides, the program will refuse to accept 
+the descriptor.
+
+Relational elements have an additional field which specifies a "transformation matrix" of four 
+nucleotides, specifying the rule for making the ``r'`` pattern from the ``r`` sequence in order 
+``A-C-G-T``. For example, the transformation matrix for a simple helix is ``TGCA``; if you allow 
+``G-U`` pairs, it is ``TGYR``. RNABOB allows ``G-U`` pairing by default and uses the ``TGYR`` 
+matrix for helical elements.
+
+For example, the explicit description of our hairpin might be:
+
+::
+
+	\
+	 		h1 0:0 NNN:NNN
+	 		r1 0:0 R:N GNAN
+	 		h2 0:0 **NC:GN**
+		 	s1 0 UUCG
+
+This describes a stem of 6 to 8 base pairs, in which the 4th pair from the bottom of the stem must 
+be a non-canonical GA pair. Note that, in general, the left side of the primary constraint for 
+helices and relational elements is redundant, and should be given as all N. In some cases it is 
+convenient to constrain the right side to require a particular base pair (GU, for instance) at one 
+position.
+
+A note on mismatches: The split format for helices and relational elements works like this. The 
+number on the left constrains the primary sequence match of the left side of the primary 
+constraint. The number on the right constrains the match of the right side of the primary 
+constraint, *after* that side has been constructed according to the sequence on the left. In other 
+words, the number on the left constrains the mismatches in primary sequence only, while the number 
+on the right will constrain the number of mispaired positions in the helix.
+
+Finally: any line that begins with a pound sign '#' is a comment line, and will not be interpreted 
+by the pattern compiler.
+
+**Options**
+
+The behavior of RNABOB can be modified by use of the following options:
+
+*Complement*: Selecting this option will cause RNABOB to search for the pattern also on the 
+complementary strands.
+
+*Skip*: This is a workaround to avoid a problem in the DNABANK. There are some sequences in the 
+database which have long stretches of ambiguous sequence (N's). Descriptors with no primary 
+sequence constraints will match these garbage sequences at many, many positions, and generate huge 
+outputs. This option toggles a search strategy that skips forward a pattern-length rather than a 
+single base when a match is found, thus printing out only a single match when overlapping matches 
+are found. 
+
+**Examples**
+
+The following example descriptors included in the source distribution 
+(http://selab.janelia.org/software/rnabob/rnabob.tar.gz):
+
+	- trna.des - a general descriptor of a tRNA structure
+	- r17.des - descriptor of the consensus binding site for the r17 phage coat protein
+	- pseudoknot.des - description of a simple pseudoknotted structure
+
+An example cosmid ``F22B7.fa`` from the *C. elegans* genome sequencing project is also provided 
+for running these descriptors against.
+
+::
+
+	\
+		# trna.des
+		#
+		# Generalized descriptor of a tRNA cloverleaf. Doesn't
+		# find them all though. 
+		#
+
+		h1 s1 h2 s2 h2' s3 h3 s4 h3' s5 h4 s6 h4' h1' s8
+
+		h1 0:2 NNNNNNN:NNNNNNN
+		h2 0:1 *NNN:NNN*
+		h3 0:1 NNNNN:NNNNN
+		h4 0:1 NNNNN:NNNNN
+		s1 0 TN
+		s2 0 NNNN**********
+		s3 0 N
+		s4 0 NNNNNN*
+		s5 0 NN********************
+		s6 0 TTC****
+		s8 0 NCCA
+
+Running RNABOB with ``trna.des`` against ``F22B7.fa`` searches the top strand of the cosmid for 
+the above motif. ``trna.des`` hits twice, once on each strand. (F22B7 has several other tRNA genes 
+in it which the pattern fails to detect - this is *not* a pattern to use for tRNA genefinding!).
+    </help> 
+    <citations>
+	<citation type="doi">10.1093/bioinformatics/6.4.325</citation>
+	<citation type="bibtex">@UNPUBLISHED{rnabob,
+author = {Eddy S.R},
+title = {RNABOB: a program to search for RNA secondary structure motifs in sequence databases},
+note = {}}</citation>
+    </citations>
+</tool>