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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
author rnateam
date Fri, 13 Jan 2017 16:48:31 -0500
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1 <tool id="locarna_pairwise_p" name="LocARNA Pairwise Probability Aligner" version="@VERSION@.0">
2 <description>
3 Partition Function and Probabilities from Pairwise Simultaneous Alignment and Folding of RNAs (LocARNA-P)
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 locarna_p
18
19 '$inputA'
20 '$inputB'
21
22 --width 60
23
24 @SCORING_ARGS@
25
26 @FOLDING_ARGS@
27
28 @HEURISTIC_ARGS@
29 #if float($Heuristics.pf_scale) != 1.0
30 --pf-scale $Heuristics.pf_scale
31 #end if
32
33 ## -------------------- other parameters
34
35 #if $Constraints.maxBPspan != -1
36 --maxBPspan $Constraints.maxBPspan
37 #end if
38
39 $Constraints.ignore_constraints
40
41 ## -------------------- probability parameters
42 $Probabilities.include_am_in_bm
43 #if float($Probabilities.min_bm_prob) != 0.0005
44 --min-bm-prob $Probabilities.min_bm_prob
45 #end if
46 #if float($Probabilities.min_am_prob) != 0.0005
47 --min-am-prob $Probabilities.min_am_prob
48 #end if
49
50 ## -------------------- output
51
52 #if not $arc_match_probs is None
53 --write-arcmatch-probs=$arc_match_probs
54 #end if
55
56 #if not $base_match_probs is None
57 --write-basematch-probs=$base_match_probs
58 #end if
59
60 @STDOUT_ARGS@
61
62 ]]></command>
63
64 <inputs>
65 <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A"
66 help="First sequence in fasta, clustal, dp_ps, or PP2.0 format"
67 />
68 <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B"
69 help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"
70 />
71
72 <param name="outputs" type="select" display="checkboxes" multiple="True"
73 label="Output options">
74 <option value="base_match_probs" selected="True">
75 Output base match probabilities</option>
76 <option value="arc_match_probs" selected="True">
77 Output arc match probabilities</option>
78 </param>
79
80 <param name="stdout_verbosity" type="select" label="Standard output verbosity">
81 <option value="--quiet">Don't report standard
82 output</option>
83 <option value="">Non verbose</option>
84 <option value="--verbose">Verbose</option>
85 </param>
86
87 <section name="Probabilities" title="Probability parameters">
88 <param name="include_am_in_bm" argument="include-am-in-bm"
89 type="boolean"
90 truevalue="--include-am-in-bm" falsevalue=""
91 label="Include arc match cases in computation of base match probabilities" />
92 <param name="min_bm_prob" argument="min-bm-prob"
93 type="float"
94 value="0.0005" min="0.0" max="1.0"
95 label="Minimal base match probability"
96 />
97 <param name="min_am_prob" argument="min-am-prob"
98 type="float"
99 value="0.0005" min="0.0" max="1.0"
100 label="Minimal arc match probability"
101 />
102 </section>
103
104 <section name="Scoring" title="Scoring parameters">
105 <expand macro="common_scoring_parameters" />
106 </section>
107
108 <section name="Folding" title="RNA folding parameters">
109 <expand macro="common_folding_parameters" />
110 <expand macro="alifold_consensus_parameter" />
111 <param name="consensus_structure" type="select" label="Consensus structure type"
112 help="Type of consensus structures written to screen and stockholm output"
113 >
114 <!-- <option value="mea">mea</option>-->
115 <option value="none">none</option>
116 <option value="alifold">alifold</option>
117 </param>
118 </section>
119
120 <section name="Heuristics" title="Heuristic parameters">
121 <expand macro="common_heuristic_parameters" />
122 <expand macro="max_diff_parameters_aln" />
123 <param name="pf_scale" argument="pf-scale"
124 type="float" value="1.0"
125 label="Scaling of the partition function."
126 help="Use (only) if standard scaling overflows." />
127 </section>
128
129 <section name="Constraints" title="Constraint parameters">
130 <expand macro="common_constraint_parameters" />
131 </section>
132
133 </inputs>
134
135 <outputs>
136 <expand macro="standard_outupt" />
137 <data format="table" name="base_match_probs" label="${tool.name} base match probabilties on ${on_string}">
138 <filter>'base_match_probs' in outputs</filter>
139 </data>
140 <data format="table" name="arc_match_probs" label="${tool.name} arc match probabilties on ${on_string}">
141 <filter>'arc_match_probs' in outputs</filter>
142 </data>
143 </outputs>
144
145 <tests>
146 <test>
147 <param name="inputA" value="tRNA_2-1.fa" />
148 <param name="inputB" value="tRNA_2-2.fa" />
149 <param name="outputs" value="arc_match_probs,base_match_probs"/>
150 <param name="min_bm_prob" value="0.01" />
151 <param name="min_am_prob" value="0.01" />
152 <output name="base_match_probs" file="tRNA_2.bmprobs" />
153 <output name="arc_match_probs" file="tRNA_2.amprobs" />
154 </test>
155 </tests>
156
157 <help><![CDATA[ **LocARNA -- Pairwise probability alignment of RNAs**
158
159 Pairwise probability alignment tool of the LocARNA suite. This tool
160 computes base and arc match probabilities from simultaneous RNA
161 folding and alignment. It can be adapted to specific needs by a broad
162 range of parameters:
163
164 * *scoring* of the alignment, e.g. influencing the cost of
165 insertions/deletions and the weight of sequence vs. structure
166 similarity.
167
168 * *RNA folding*, which control the secondary RNA structure prediciton.
169
170 * *heuristics*, which trade alignment accuracy vs. computation
171 speed. The huge complexity of simultaneous alignment and folding
172 generally requires some heuristics for reasonable computation times.
173 Some alignment instances and alignment modes will require relaxation
174 of the default heuristics; in particular, local, constrained, and free end gap
175 alignment, will often require turning off the "maximal difference for
176 alignment traces" heuristic.
177
178 * *constraints*, which can be applied to include prior knowledge to
179 improve the quality of results and/or speed of computation.
180
181 **Input.**
182
183 Input consists of two sequences or alignments, which are specified in
184 fasta, clustal, stockholm, or LocARNA pp format.
185
186 Optionally, one can specify structure and anchor constraints in these
187 input files.
188
189 **Output.**
190
191 The tool writes two tables of base match and arc match probabilities, respectively. Rows
192 in the base match probabilities table consist of
193
194 i j p
195
196 where p is the probability of matching position i in the first sequence to position j in the second sequence.
197
198 For arc matchs, the table contains rows
199
200 i j k l p
201
202 where p is the probability of matching the base pair (i,j) of sequence one to (k,l) of sequence two.
203
204 Moreover, the partition function and further information can be written to standard out.
205
206 For more information, see
207 .. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
208 ]]></help>
209
210 <expand macro="citations" />
211
212 </tool>