Mercurial > repos > rnateam > rnabob

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob commit 1527e05bcd748a2b3cef22e0e356697066a55635
author rnateam
date Sat, 11 Nov 2017 15:08:06 -0500
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1 <tool id="rbc_rnabob" name="RNABOB" version="2.2.1.0">
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2 <description>Fast Pattern searching for RNA secondary structures</description>
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3
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4 <requirements>
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5 <requirement type="package" version="2.2.1">rnabob</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
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9 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
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10 </stdio>
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11 <version_command>echo "2.2.1"</version_command>
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12 <command>
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13 <![CDATA[
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14 rnabob
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15 -q
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16 $fancy
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17 $compStrands
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18 $skipOverlapping
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19 $descriptorFile
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20 $sequenceFile > $stdout
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21 ]]>
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22 </command>
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23 <inputs>
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24 <param name="descriptorFile" type="data" format="txt" multiple="false" label="Motif Descriptor File" help="This file contains the description of the motif for which to search"/>
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25 <param name="sequenceFile" type="data" format="fasta" multiple="false" label="Sequence File" help="This file specifies the sequence in which the motif will be searched"/>
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26 <param name="compStrands" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Also search on complementary strands" help="-c : Search both strands of the supplied sequence"/>
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27 <param name="skipOverlapping" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Skip overlapping matches" help="-s : This is a workaround to avoid a problem in the DNABANK, overlapping matches will be ignored"/>
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28 <param name="fancy" type="boolean" checked="false" truevalue="-F" falsevalue="" label="Show Alignments" help="Display full alignments to pattern"/>
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29 </inputs>
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30 <outputs>
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31 <data format="txt" name="stdout" label="${tool.name} on ${on_string}" />
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="descriptorFile" value="r17.des" />
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36 <param name="sequenceFile" value="F22B7.fa" />
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37 <param name="compStrands" value="True" />
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38 <param name="skipOverlapping" value="False" />
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39 <param name="fancy" value="False" />
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40 <output name="stdout" file="r17.bob" />
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41 </test>
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42 <test>
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43 <param name="descriptorFile" value="trna.des" />
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44 <param name="sequenceFile" value="F22B7.fa" />
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45 <param name="compStrands" value="True" />
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46 <param name="skipOverlapping" value="False" />
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47 <param name="fancy" value="False" />
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48 <output name="stdout" file="trna.bob" />
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49 </test>
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50 </tests>
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51 <help>
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52 <![CDATA[
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53 **What RNABOB does**
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54
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55 RNABOB allows searching a sequence database for RNA structural motifs.
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56 The probe motif is specified in a *descriptor* file,
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57 which describes its primary sequence, secondary structure, and tertiary constraints.
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58 The source in its original packaging can be found at http://selab.janelia.org/software/#rnabob.
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59
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60 -----
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61
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62 **Sequence database format**
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63
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64 RNABOB is currently restricted to reading sequence files in FASTA format.
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65 The command line version of RNABOB can also read sequence files in GCG, EMBL, GenBank and other formats.
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66
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67 -----
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68
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69 **Descriptor file syntax**
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70
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71 The descriptor file syntax is fairly powerful, and allows a great deal of freedom for specifying
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72 RNA motifs. The syntax is therefore a bit complicated.
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73
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74 The descriptor file has two parts: a **topology** description and an **explicit** description.
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75
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76 The first non-blank, non-comment line of the file is the topology description. It defines the
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77 order of occurrence of a series of single-stranded, double-stranded and related elements. Each
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78 element must be given a unique name (a number, typically) and must be prefixed with '**s**',
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79 '**h**', or '**r**', indicating single-strand, helical, or a relational element. Helical and
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80 relational elements are paired to other elements, which are suffixed by a prime, **\'**.
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81
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82 For example::
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83
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84 \
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85 h1 s1 h1'
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86
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87 describes a hairpin loop structure with a simple helix and single-stranded loop. If the helix
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88 always contained a non-canonical base pair at one position, the topology coud be described as::
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89
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90 \
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91 h1 r1 h2 s1 h2' r1' h1'
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92
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93 where r1,r1' indicate a correlation, where the sequence r1 constrains the sequence of r1'.
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94 (Helices are a special case of this.)
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95
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96 The remaining non-comment, non-blank lines are explicit descriptions of each element in turn. Each
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97 line contains 3 or 4 fields, separated by tabs or blank space. The first field is the name of the
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98 element, from the topology description. The second field is the number of mismatches allowed in
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99 this element. The third field is the primary sequence constraint to apply to this element.
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100
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101 Helices and relational element pairs are specified on a single line rather than two. Mismatches
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102 and primary sequence constraints are given as pairs, separated by a colon '**:**'. The left side
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103 is the constraint applied to the upstream element, and the right side is applied to the downstream
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104 elements.
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105
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106 The primary sequence constraint is given as a sequence of nucleotides. Any IUPAC single-letter
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107 code is recognized, including N if the position can have any base identity. Allowed length
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108 variations are specified with asterisks ``'*'``, where each ``*`` will allow either 0 or 1 N at
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109 that position.
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110
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111 For example::
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112
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113 \
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114 GGAGG******NNNAUG
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115
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116 specifies a GGAGG Shine/Dalgarno site and an AUG initiation codon, separated by a spacer of 3 to 9
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117 nucleotides of any sequence.
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118
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119 An alternative syntax can be used for very long gaps::
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120
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121 \
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122 GGAGG[10]NNNAUG is the same as GGAGG**********NNNAUG
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123
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124 Be careful defining variable length helices and relational elements; if the number and type (gap
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125 or identity) of position do not match on left and right sides, the program will refuse to accept
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126 the descriptor.
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127
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128 Relational elements have an additional field which specifies a "transformation matrix" of four
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129 nucleotides, specifying the rule for making the ``r'`` pattern from the ``r`` sequence in order
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130 ``A-C-G-T``. For example, the transformation matrix for a simple helix is ``TGCA``; if you allow
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131 ``G-U`` pairs, it is ``TGYR``. RNABOB allows ``G-U`` pairing by default and uses the ``TGYR``
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132 matrix for helical elements.
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133
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134 For example, the explicit description of our hairpin might be:
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135
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136 ::
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137
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138 \
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139 h1 0:0 NNN:NNN
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140 r1 0:0 R:N GNAN
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141 h2 0:0 **NC:GN**
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142 s1 0 UUCG
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143
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144 This describes a stem of 6 to 8 base pairs, in which the 4th pair from the bottom of the stem must
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145 be a non-canonical GA pair. Note that, in general, the left side of the primary constraint for
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146 helices and relational elements is redundant, and should be given as all N. In some cases it is
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147 convenient to constrain the right side to require a particular base pair (GU, for instance) at one
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148 position.
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149
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150 A note on mismatches: The split format for helices and relational elements works like this. The
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151 number on the left constrains the primary sequence match of the left side of the primary
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152 constraint. The number on the right constrains the match of the right side of the primary
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153 constraint, *after* that side has been constructed according to the sequence on the left. In other
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154 words, the number on the left constrains the mismatches in primary sequence only, while the number
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155 on the right will constrain the number of mispaired positions in the helix.
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156
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157 Finally: any line that begins with a pound sign '#' is a comment line, and will not be interpreted
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158 by the pattern compiler.
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159
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160 **Options**
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161
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162 The behavior of RNABOB can be modified by use of the following options:
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163
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164 *Complement*: Selecting this option will cause RNABOB to search for the pattern also on the
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165 complementary strands.
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166
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167 *Skip*: This is a workaround to avoid a problem in the DNABANK. There are some sequences in the
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168 database which have long stretches of ambiguous sequence (N's). Descriptors with no primary
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169 sequence constraints will match these garbage sequences at many, many positions, and generate huge
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170 outputs. This option toggles a search strategy that skips forward a pattern-length rather than a
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171 single base when a match is found, thus printing out only a single match when overlapping matches
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172 are found.
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173
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174 **Examples**
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175
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176 The following example descriptors included in the source distribution
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177 (http://selab.janelia.org/software/rnabob/rnabob.tar.gz):
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178
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179 - trna.des - a general descriptor of a tRNA structure
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180 - r17.des - descriptor of the consensus binding site for the r17 phage coat protein
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181 - pseudoknot.des - description of a simple pseudoknotted structure
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182
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183 An example cosmid ``F22B7.fa`` from the *C. elegans* genome sequencing project is also provided
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184 for running these descriptors against.
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185
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186 ::
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187
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188 \
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189 # trna.des
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190 #
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191 # Generalized descriptor of a tRNA cloverleaf. Doesn't
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192 # find them all though.
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193 #
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194
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195 h1 s1 h2 s2 h2' s3 h3 s4 h3' s5 h4 s6 h4' h1' s8
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196
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197 h1 0:2 NNNNNNN:NNNNNNN
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198 h2 0:1 *NNN:NNN*
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199 h3 0:1 NNNNN:NNNNN
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200 h4 0:1 NNNNN:NNNNN
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201 s1 0 TN
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202 s2 0 NNNN**********
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203 s3 0 N
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204 s4 0 NNNNNN*
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205 s5 0 NN********************
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206 s6 0 TTC****
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207 s8 0 NCCA
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208
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209 Running RNABOB with ``trna.des`` against ``F22B7.fa`` searches the top strand of the cosmid for
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210 the above motif. ``trna.des`` hits twice, once on each strand. (F22B7 has several other tRNA genes
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211 in it which the pattern fails to detect - this is *not* a pattern to use for tRNA genefinding!).
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212 ]]>
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213 </help>
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214 <citations>
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215 <citation type="doi">10.1093/bioinformatics/6.4.325</citation>
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216 <citation type="bibtex">@UNPUBLISHED{rnabob,
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217 author = {Eddy S.R},
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218 title = {RNABOB: a program to search for RNA secondary structure motifs in sequence databases},
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219 note = {}}</citation>
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220 </citations>
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221 </tool>