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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 18:47:18 -0500
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1 <tool id="locarna_multiple" name="LocARNA Multiple Aligner (mlocarna)" version="@VERSION@.0">
2 <description>
3 Multiple 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 mlocarna
18
19 '$input_data'
20 #if 'stockholm' in str($outputs).split(","):
21 --stockholm
22 #end if
23
24 --tgtdir mlocarna_results
25 --width 60
26
27 ## -------------------- alignment mode and specific options
28
29 #if str($alignment_mode.alignment_mode_selector) == "global_locarna"
30 $alignment_mode.free_endgaps
31 #else if str($alignment_mode.alignment_mode_selector) == "local_locarna"
32 --sequ-local on
33 #else if str($alignment_mode.alignment_mode_selector) == "probabilistic"
34 --probabilistic
35 $alignment_mode.consistency_transformation
36
37 #if str($alignment_mode.iterate) == "true"
38 --iterate
39 --iterations $alignment_mode.iterations
40 #end if
41 #else if str($alignment_mode.alignment_mode_selector) == "sparse"
42 --sparse
43 #end if
44
45 ## -------------------- scoring parameters
46
47 --indel $Scoring.indel
48 --indel-opening $Scoring.indel_opening
49 --struct-weight $Scoring.struct_weight
50 --tau $Scoring.tau
51
52 #if str($Scoring.sequence_score.sequence_score_selector) == "match"
53 --match $Scoring.sequence_score.match
54 --mismatch $Scoring.sequence_score.mismatch
55 #else if str($Scoring.sequence_score.sequence_score_selector) == "ribosum"
56 --use-ribosum true
57 #else if str($Scoring.sequence_score.sequence_score_selector) == "ribofit"
58 --ribofit true
59 #end if
60
61 ## -------------------- folding parameters
62
63 #if $Folding.plfold_span>=0
64 --plfold-span $Folding.plfold_span
65 --plfold-winsize $Folding.plfold_winsize
66 #end if
67
68 #if float($Folding.rnafold_temperature) != 37.0
69 --rnafold-temperature $Folding.rnafold_temperature
70 #end if
71
72 $Folding.alifold_consensus_dp
73
74 ## -------------------- heuristic parameters
75
76 -p $Heuristics.min_prob
77 --max-diff-am $Heuristics.max_diff_am
78 --max-diff $Heuristics.max_diff
79 --max-diff-at-am $Heuristics.max_diff_at_am
80 --max-bps-length-ratio $Heuristics.max_bps_length_ratio
81
82
83 ## -------------------- other parameters
84
85 #if str($Constraint.bed_anchors.bed_anchors_selector) == "yes"
86 --anchor-constraints $Constraint.bed_anchors.bed_anchors_file
87 #end if
88
89 $Constraint.lonely_pairs
90
91 #if $Constraint.maxBPspan != -1
92 --maxBPspan $Constraint.maxBPspan
93 #end if
94
95 $Constraint.ignore_constraints
96
97 $stdout_verbosity
98
99 #if str($stdout_verbosity) != "--quiet":
100 > '$stdout'
101 #end if
102
103 #if 'clustal_strict' in str($outputs).split(",")
104 && grep -v '^#' mlocarna_results/results/result.aln > mlocarna_results/results/result.strict-aln
105 #end if
106
107 ]]></command>
108
109 <inputs>
110 <conditional name="input_data_type">
111 <param name="input_data_type_selector" type="select" label="Input type">
112 <option value="fasta">Fasta input (strict)</option>
113 <option value="text">Fasta-like input with LocARNA constraints</option>
114 </param>
115 <when value="fasta">
116 <param name="input_data" type="data" format="fasta" label="Sequence input"
117 help="Sequence input in pure fasta format"
118 />
119 </when>
120 <when value="text">
121 <param name="input_data" type="data" format="text" label="Sequence input"
122 help="Sequence input in fasta format with locarna-specific extensions"
123 />
124 </when>
125 </conditional>
126 <conditional name="alignment_mode">
127 <param name="alignment_mode_selector" type="select" label="Alignment mode"
128 help="Note that local alignment mode usually requires to turn off
129 the 'max-diff' heuristic (maximal difference for alignment traces)."
130 >
131 <option value="global_locarna">Global alignment
132 (LocARNA)</option>
133 <option value="local_locarna">Local alignment (LocARNA)</option>
134 <option value="probabilistic">Probabilistic alignment (LocARNA-P)</option>
135 <option value="sparse">Global alignment (SPARSE)</option>
136 </param>
137 <when value="global_locarna">
138 <param name="free_endgaps" type="select" label="Free endgaps"
139 help="Specify whether gaps at the ends (all, 5', or 3' ends)
140 of the sequences should be penalized or allowed for free.">
141 <option value="">No free endgaps</option>
142 <option value="--free-endgaps">Free endgaps</option>
143 <option value="--free-endgaps-5">Free endgaps, only 5'</option>
144 <option value="--free-endgaps-3">Free endgaps, only 3'</option>
145 </param>
146 </when>
147 <when value="local_locarna">
148 </when>
149 <when value="probabilistic">
150 <param name="consistency_transformation" type="boolean"
151 truevalue="--consistency-transformation" falsevalue=""
152 checked="true" label="Consistency transformation"
153 help="--consistency-transformation" />
154 <param name="iterate" type="boolean"
155 truevalue="true" falsevalue="false"
156 checked="false" label="Iterative refinement"
157 help="--iterate" />
158 <param name="iterations" type="integer"
159 value="1" label="Number of refinement iterations"
160 help="--iterations num" />
161 </when>
162 <when value="sparse" />
163 </conditional>
164
165 <param name="outputs" type="select" display="checkboxes" multiple="True"
166 label="Output options">
167 <option value="clustal_strict" selected="True">Output alignment
168 in ClustalW format</option>
169 <option value="clustal" selected="False">Output alignment
170 in constraint-annotated ClustalW format</option>
171 <option value="stockholm" selected="False">Output
172 alignment in Stockholm format</option>
173 <option value="pp" selected="False">Output
174 alignment in LocARNA's PP 2.0 format</option>
175 <option value="mlocarna_results" selected="False">
176 Output LocARNA results archive (tar.gz)</option>
177 </param>
178
179 <param name="stdout_verbosity" type="select" label="Standard output verbosity">
180 <option value="--quiet">Don't report standard
181 output</option>
182 <option value="">Non verbose</option>
183 <option value="--verbose">Verbose</option>
184 <option value="--moreverbose">More verbose</option>
185 </param>
186
187 <section name="Scoring" title="Scoring parameters">
188 <expand macro="common_scoring_parameters" />
189 </section>
190
191 <section name="Folding" title="RNA folding parameters">
192 <expand macro="plfolding_parameters" />
193 <expand macro="common_folding_parameters" />
194 <expand macro="alifold_consensus_parameter" />
195 </section>
196
197 <section name="Heuristics" title="Heuristic parameters">
198 <expand macro="common_heuristic_parameters" />
199 </section>
200
201 <section name="Constraint" title="Constraint parameters">
202 <expand macro="bed_anchors" />
203 <expand macro="constraints" />
204 </section>
205 </inputs>
206
207 <outputs>
208 <expand macro="common_outputs" />
209 </outputs>
210
211 <tests>
212 <test>
213 <param name="input_data" value="archaea.fa" />
214 <param name="stdout_verbosity" value="" />
215 <output name="stdout" file="archaea-default.stdout" />
216 </test>
217 <test>
218 <param name="input_data" value="haca.snoRNA.fa" />
219 <param name="stdout_verbosity" value="" />
220 <output name="stdout" file="haca.snoRNA-default.stdout" />
221 </test>
222 <test>
223 <param name="input_data" value="archaea.fa" />
224 <param name="stdout_verbosity" value="" />
225 <param name="outputs" value="clustal" />
226 <param name="alignment_mode_selector" value="probabilistic" />
227 <output name="clustal" file="archaea-probabilistic.aln" />
228 </test>
229 </tests>
230
231 <help><![CDATA[ **MLocARNA -- Multiple alignment of RNAs**
232
233 MLocARNA is the (general, progressive) multiple RNA alignment tool of
234 the LocARNA suite. It supports several alignment modes and can be
235 adapted to specific needs by a broad range of parameters. Thus, there
236 are parameters for
237
238 * *scoring* of the alignment, e.g. influencing the cost of
239 insertions/deletions and the weight of sequence vs. structure
240 similarity.
241
242 * *RNA folding*, which control the secondary RNA structure prediciton.
243
244 * *heuristics*, which trade alignment accuracy vs. computation
245 speed. The huge complexity of simultaneous alignment and folding
246 generally requires some heuristics for reasonable computation times.
247 Some alignment instances and alignment modes will require relaxation
248 of the default heuristics; in particular, local, constrained, and free end gap
249 alignment, will often require turning off the "maximal difference for
250 alignment traces" heuristic.
251
252 * *constraints*, which can be applied to include prior knowledge to
253 improve the quality of results and/or speed of computation.
254
255 Technically, mlocarna constructs multiple alignments progressively
256 based on pairwise alignments by locarna, locarna-p, or sparse, which
257 perform variants of simultaneous RNA folding and alignment.
258
259 **Input.**
260 Sequences can be given in plain fasta format like::
261
262 >fruA
263 CCUCGAGGGGAACCCGAAAGGGACCCGAGAGG
264 >fdhA
265 CGCCACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAGGUGGCG
266 >vhuU
267 AGCUCACAACCGAACCCAUUUGGGAGGUUGUGAGCU
268
269 Morover, mlocarna supports structure constraints for folding and anchor
270 constraints for alignment. Both types of constraints can be specified
271 in extension of the standard fasta format via 'constraint
272 lines'. Fasta-ish input with constraints looks like this::
273
274 >A
275 GACCCUGGGAACAUUAACUACUCUCGUUGGUGAUAAGGAACA
276 ..((.(....xxxxxx...................))).xxx #S
277 ..........000000.......................111 #1
278 ..........123456.......................123 #2
279 >B
280 ACGGAGGGAAAGCAAGCCUUCUGCGACA
281 .(((....xxxxxx.......))).xxx #S
282 ........000000...........111 #1
283 ........123456...........123 #2
284
285 The same anchor constraints (like by the lines tagged #1, #2) can
286 alternatively be specified in bed format by the entries::
287
288 A 10 16 first_box
289 B 8 14 first_box
290 A 39 42 ACA-box
291 B 25 28 ACA-box
292
293 where anchor regions (boxes) have arbitrary but matching names
294 and contig/sequence names correspond to the sequence names
295 of the fasta(-like) input.
296
297
298 **Output.**
299
300 The final alignment is reported in standard and/or variants of the
301 clustal and stockholm format. Moreover, an archive with final and
302 intermediary results of the mlocarna run can be returned.
303
304
305 For more information, see
306 .. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
307 ]]></help>
308
309 <expand macro="citations" />
310
311 </tool>