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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
author bgruening
date Wed, 28 Dec 2016 18:48:14 -0500
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1 <tool id="locarna_pairwise" name="LocARNA Pairwise Aligner" version="@VERSION@.0">
2 <description>
3 Pairwise Simultaneous Alignment and Folding of RNAs
4 </description>
5
6 <macros>
7 <import>macros.xml</import>
8 </macros>
9
10 <expand macro="requirements" />
11
12 <expand macro="stdio" />
13
14 <expand macro="version" />
15
16 <command><![CDATA[
17 #if str($alignment_mode.alignment_mode_selector) == "sparse"
18 sparse
19 #else
20 locarna
21 #end if
22
23 '$inputA'
24 '$inputB'
25
26 --width 60
27
28 ## -------------------- alignment mode and specific options
29
30 #if str($alignment_mode.alignment_mode_selector) == "global_locarna"
31 #if str($alignment_mode.free_endgaps) != "----"
32 --free-endgaps $alignment_mode.free_endgaps
33 #end if
34 #else if str($alignment_mode.alignment_mode_selector) == "local_locarna"
35 --sequ-local on
36 #else if str($alignment_mode.alignment_mode_selector) == "structure_local_locarna"
37 --struct-local on
38 #else if str($alignment_mode.alignment_mode_selector) == "structure_sequence_local_locarna"
39 --sequ-local on
40 --struct-local on
41 #end if
42
43 ## -------------------- scoring parameters
44
45 --indel $Scoring.indel
46 --indel-opening $Scoring.indel_opening
47 --struct-weight $Scoring.struct_weight
48 --tau $Scoring.tau
49
50 #if str($Scoring.sequence_score.sequence_score_selector) == "match"
51 --match $Scoring.sequence_score.match
52 --mismatch $Scoring.sequence_score.mismatch
53 #else if str($Scoring.sequence_score.sequence_score_selector) == "ribosum"
54 --use-ribosum true
55 #else if str($Scoring.sequence_score.sequence_score_selector) == "ribofit"
56 --ribofit true
57 #end if
58
59 ## -------------------- folding parameters
60
61 #if float($Folding.rnafold_temperature) != 37.0
62 --rnafold-temperature $Folding.rnafold_temperature
63 #end if
64
65 $Folding.alifold_consensus_dp
66 --consensus-structure $Folding.consensus_structure
67
68 ## -------------------- heuristic parameters
69
70 -p $Heuristics.min_prob
71 --max-diff-am $Heuristics.max_diff_am
72 --max-diff $Heuristics.max_diff
73 --max-diff-at-am $Heuristics.max_diff_at_am
74
75 #if float($Heuristics.max_bps_length_ratio) != 0.0
76 --max-bps-length-ratio $Heuristics.max_bps_length_ratio
77 #end if
78
79 ## -------------------- other parameters
80
81 $Constraint.lonely_pairs
82
83 #if $Constraint.maxBPspan != -1
84 --maxBPspan $Constraint.maxBPspan
85 #end if
86
87 $Constraint.ignore_constraints
88
89 ## -------------------- output
90
91 #if 'stockholm' in str($outputs).split(",")
92 --stockholm '$stockholm'
93 #end if
94 #if 'clustal' in str($outputs).split(",")
95 --clustal '$clustal'
96 #end if
97 #if 'clustal_strict' in str($outputs).split(",") and (not 'clustal' in str($outputs).split(","))
98 --clustal '$clustal_strict'
99 #end if
100 #if 'pp' in str($outputs).split(",")
101 --pp '$pp'
102 #end if
103
104 $stdout_verbosity
105
106 #if str($stdout_verbosity) != "--quiet":
107 > '$stdout'
108 #end if
109
110 #if 'clustal' in str($outputs).split(",") and 'clustal_strict' in str($outputs).split(",")
111 && cp $clustal $clustal_strict
112 #end if
113
114 #if 'clustal_strict' in str($outputs).split(",")
115 && sed -i '/\^#/d' '$clustal_strict'
116 #end if
117
118 ]]></command>
119
120 <inputs>
121 <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A"
122 help="First sequence in fasta, clustal, dp_ps, or PP2.0 format"
123 />
124 <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B"
125 help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"
126 />
127 <conditional name="alignment_mode">
128 <param name="alignment_mode_selector" type="select" label="Alignment mode"
129 help="Note that local alignment mode usually requires to turn off
130 the 'max-diff' heuristic (maximal difference for alignment traces)."
131 >
132 <option value="global_locarna">Global alignment
133 (LocARNA)</option>
134 <option value="local_locarna">Local alignment (LocARNA)</option>
135 <option value="sparse">Global alignment (SPARSE)</option>
136 <option value="structure_sequence_local_locarna">
137 Structure and sequence local alignment (LocARNA)
138 </option>
139 <option value="structure_local_locarna">
140 Structure local, sequence global alignment (LocARNA)
141 </option>
142 </param>
143 <when value="global_locarna">
144 <param name="free_endgaps" type="select" label="Free endgaps"
145 help="Specify whether gaps at the ends (all, 5', or 3' ends)
146 of the sequences should be penalized or allowed for free.">
147 <option value="----">None</option>
148 <option value="++++">All</option>
149 <option value="+-+-">5' ends</option>
150 <option value="-+-+">3' ends</option>
151 <option value="++--">first sequence</option>
152 <option value="--++">second sequence</option>
153 <option value="+---">sequence A, 5' end</option>
154 <option value="-+--">sequence A, 3' end</option>
155 <option value="--+-">sequence B, 5' end</option>
156 <option value="---+">sequence B, 3' end</option>
157 </param>
158 </when>
159 <when value="local_locarna">
160 </when>
161 <when value="sparse" />
162 <when value="structure_sequence_local_locarna" />
163 <when value="structure_local_locarna" />
164 </conditional>
165
166 <param name="outputs" type="select" display="checkboxes" multiple="True"
167 label="Output options">
168 <option value="clustal_strict" selected="True">Output alignment
169 in ClustalW format</option>
170 <option value="clustal" selected="False">Output alignment
171 in constraint-annotated ClustalW format</option>
172 <option value="stockholm" selected="False">Output
173 alignment in Stockholm format</option>
174 <option value="pp" selected="False">Output
175 alignment in LocARNA's PP 2.0 format</option>
176 </param>
177
178 <param name="stdout_verbosity" type="select" label="Standard output verbosity">
179 <option value="--quiet">Don't report standard
180 output</option>
181 <option value="">Non verbose</option>
182 <option value="--verbose">Verbose</option>
183 </param>
184
185 <section name="Scoring" title="Scoring parameters">
186 <expand macro="common_scoring_parameters" />
187 </section>
188
189 <section name="Folding" title="RNA folding parameters">
190 <expand macro="common_folding_parameters" />
191 <expand macro="alifold_consensus_parameter" />
192 <param name="consensus_structure" type="select" label="Consensus structure type"
193 help="Type of consensus structures written to screen and stockholm output"
194 >
195 <!-- <option value="mea">mea</option>-->
196 <option value="none">none</option>
197 <option value="alifold">alifold</option>
198 </param>
199 </section>
200
201 <section name="Heuristics" title="Heuristic parameters">
202 <expand macro="common_heuristic_parameters" />
203 </section>
204
205 <section name="Constraint" title="Constraint parameters">
206 <expand macro="constraints" />
207 </section>
208 </inputs>
209
210 <outputs>
211 <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}">
212 <filter>stdout_verbosity != '--quiet'</filter>
213 </data>
214 <data format="clustal" name="clustal"
215 label="${tool.name} alignment (annotated clustal) on ${on_string}">
216 <filter>'clustal' in outputs</filter>
217 </data>
218 <data format="clustal" name="clustal_strict"
219 label="${tool.name} alignment (clustal) on ${on_string}">
220 <filter>'clustal_strict' in outputs</filter>
221 </data>
222 <data format="stockholm" name="stockholm"
223 label="${tool.name} alignment (stockholm) on ${on_string}">
224 <filter>'stockholm' in outputs</filter>
225 </data>
226 <data format="txt" name="pp"
227 label="${tool.name} alignment (PP 2.0) on ${on_string}">
228 <filter>'pp' in outputs</filter>
229 </data>
230 </outputs>
231
232 <tests>
233 <test>
234 <param name="inputA" value="tRNA_2-1.fa" />
235 <param name="inputB" value="tRNA_2-2.fa" />
236 <param name="outputs" value="clustal" />
237 <output name="clustal" file="tRNA_2.aln" />
238 </test>
239 </tests>
240
241 <help><![CDATA[ **LocARNA -- Pairwise alignment of RNAs**
242
243 Pairwise RNA alignment tools of the LocARNA suite (locarna,
244 sparse). These tools perform variants of simultaneous RNA folding and
245 alignment. They can be adapted to specific needs by a broad range of
246 parameters:
247
248 * *scoring* of the alignment, e.g. influencing the cost of
249 insertions/deletions and the weight of sequence vs. structure
250 similarity.
251
252 * *RNA folding*, which control the secondary RNA structure prediciton.
253
254 * *heuristics*, which trade alignment accuracy vs. computation
255 speed. The huge complexity of simultaneous alignment and folding
256 generally requires some heuristics for reasonable computation times.
257 Some alignment instances and alignment modes will require relaxation
258 of the default heuristics; in particular, local, constrained, and free end gap
259 alignment, will often require turning off the "maximal difference for
260 alignment traces" heuristic.
261
262 * *constraints*, which can be applied to include prior knowledge to
263 improve the quality of results and/or speed of computation.
264
265 **Input.**
266
267 Input consists of two sequences or alignments, which are specified in
268 fasta, clustal, stockholm, or LocARNA pp format.
269
270 Optionally, one can specify structure and anchor constraints in these
271 input files.
272
273 **Output.**
274
275 The final pairwise alignment is reported in standard and/or variants of the
276 clustal and stockholm format, as well as LocARNA's own pp format.
277
278 For more information, see
279 .. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
280 ]]></help>
281
282 <expand macro="citations" />
283
284 </tool>