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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 16:49:16 -0500
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children e66514da3a99
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-1:000000000000 0:e91e4f48875e
1 <tool id="locarna_exparnap" name="LocARNA Exact Matcher" version="@VERSION@.0">
2 <description>
3 Pairwise Simultaneous Matching and Folding of RNAs (ExpaRNA-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 exparna_p
18
19 '$inputA'
20 '$inputB'
21
22 ## -------------------- scoring parameters
23 #
24 $Scoring.no_stacking
25 --alpha_1 $Scoring.alpha_1
26 --alpha_2 $Scoring.alpha_2
27 --alpha_3 $Scoring.alpha_3
28 --struct-mismatch-score $Scoring.struct_mismatch_score
29
30 @HEURISTIC_ARGS@
31 --prob_unpaired_in_loop_threshold $Heuristics.prob_unpaired_in_loop_threshold
32 --prob_basepair_in_loop_threshold $Heuristics.prob_basepair_in_loop_threshold
33
34 @CONSTRAINT_ARGS@
35
36 ## -------------------- other parameters
37 #
38 #if str($Other.subopt.subopt_selector) == "on"
39 --diff-to-opt-score $Other.subopt.diff_to_opt_score
40 --number-of-EPMs $Other.subopt.number_of_EPMs
41 #end if
42
43 --min-score $Other.min_score
44
45 $Other.inexact_struct_match
46 $Other.add_filter
47 $Other.no_chaining
48 --out-min-prob $Other.out_min_prob
49
50 ## -------------------- output
51
52 #if 'postscript' in str($outputs).split(",")
53 --output-ps
54 --PS_fileA '$ps_fileA'
55 --PS_fileB '$ps_fileB'
56 #end if
57
58 #if 'anchors-fasta' in str($outputs).split(",")
59 --output-locarna '$anchors_fasta'
60 #end if
61
62 #if 'anchors-pp' in str($outputs).split(",")
63 --output-anchor-pp anchors_pp
64 #end if
65
66 #if 'clustal' in str($outputs).split(",")
67 --output-clustal '$clustal'
68 #end if
69
70 #if 'epm_list' in str($outputs).split(",")
71 --output-epm-list '$epm_list'
72 #end if
73
74 #if 'chained_epm_list' in str($outputs).split(",")
75 --output-chained-epm-list '$chained_epm_list'
76 #end if
77
78 @STDOUT_ARGS@
79
80 ## -------------------- post processing
81
82 #if 'anchors-pp' in str($outputs).split(",")
83 && mv anchors_pp_A.pp '$anchors_ppA'
84 && mv anchors_pp_B.pp '$anchors_ppB'
85 #end if
86
87 ]]></command>
88
89 <inputs>
90 <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A"
91 help="First sequence in fasta, clustal, dp_ps, or PP2.0 format"
92 />
93 <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B"
94 help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"
95 />
96
97 <param name="outputs" type="select" display="checkboxes" multiple="True"
98 label="Output options">
99 <option value="postscript" selected="False">Best EPM chain
100 as colored postscript</option>
101 <option value="anchors-fasta" selected="False">Fasta with anchor
102 constraints from chaining</option>
103 <option value="anchors-pp" selected="False">LocARNA PP
104 files merging input PPs and anchor constraints from
105 chaining</option>
106 <option value="clustal" selected="False">Chain as
107 alignment in Clustal format</option>
108 <option value="epm_list" selected="False">List of the found EPMs</option>
109 <option value="chained_epm_list" selected="False">List of
110 EPMs in the best chain</option>
111 </param>
112
113 <param name="stdout_verbosity" type="select" label="Standard output verbosity">
114 <option value="--quiet">Don't report standard
115 output</option>
116 <option value="" selected="True">Non verbose</option>
117 <option value="--verbose">Verbose</option>
118 </param>
119
120 <section name="Scoring" title="Scoring parameters">
121 <param argument="alpha_1"
122 type="integer" value="1" min="0" max="50"
123 label="Sequence score factor"
124 />
125 <param argument="alpha_2"
126 type="integer" value="5" min="0" max="50"
127 label="Structure score factor"
128 />
129 <param name="no_stacking" argument="no-stacking" type="boolean"
130 truevalue="" falsevalue="--no-stacking"
131 label="Add stacking terms"
132 />
133 <param argument="alpha_3"
134 type="integer" value="5" min="0" max="50"
135 label="Stacking score factor"
136 />
137 <param name="struct_mismatch_score" argument="struct-mismatch-score"
138 type="integer" value="-10" min="-100" max="0"
139 label="Score for nucleotide mismatch in base pair match"
140 />
141 </section>
142
143 <section name="Folding" title="RNA folding parameters">
144 <expand macro="common_folding_parameters" />
145 </section>
146
147 <section name="Heuristics" title="Heuristic parameters">
148 <expand macro="common_heuristic_parameters" />
149 <expand macro="max_diff_parameters" />
150 <expand macro="in_loop_ratio_parameters" />
151 <expand macro="exparnap_in_loop_parameters" />
152 </section>
153
154 <section name="Constraints" title="Constraint parameters">
155 <expand macro="common_constraint_parameters" />
156 </section>
157
158
159 <section name="Other" title="Other parameters">
160 <conditional name="subopt">
161 <param name="subopt_selector" type="select"
162 label="Suboptimal traceback of EPMs (exact pattern matches)"
163 help="(--subopt)">
164 <option value="off">Enumerate only optimal
165 EPMs</option>
166 <option value="on">Perform suboptimal traceback of EPMs</option>
167 </param>
168 <when value="off" />
169 <when value="on">
170 <param name="diff_to_opt_score" argument="diff-to-opt-score"
171 type="integer" value="-1" min="-20" max="0"
172 label="Maximum score difference to optimum" />
173 <param name="number_of_EPMs" argument="number-of-EPMs"
174 type="integer" value="100" min="1" max="10000"
175 label="Maximal number of EPMs" />
176 </when>
177 </conditional>
178
179 <param name="min_score" argument="min-score"
180 type="integer" value="30" min="0" max="1000"
181 label="Minimum score of EPM" />
182
183 <param name="inexact_struct_match" argument="inexact-struct-match" type="boolean"
184 truevalue="--inexact-struct-match" falsevalue=""
185 label="Allow inexact structure matches"/>
186
187 <param name="add_filter" argument="add-filter" type="boolean"
188 truevalue="--add-filter" falsevalue="" checked="False"
189 label="Apply an additional filter to enumerate only
190 EPMs that are maximally extended (only inexact)"/>
191
192 <param name="no_chaining" argument="no-chaining" type="boolean"
193 truevalue="" falsevalue="--no-chaining" checked="True"
194 label="Find best overall chain by chaining"/>
195
196 <param name="out_min_prob" argument="out-min-prob"
197 type="float" value="0.0005" min="0" max="1"
198 label="Minimal probability in output (min-prob overrides if smaller)"/>
199
200 </section>
201 </inputs>
202
203 <outputs>
204 <expand macro="standard_outupt" />
205 <data format="ps" name="ps_fileA"
206 label="${tool.name} chain in RNA 1 (postscript) on ${on_string}">
207 <filter>'postscript' in outputs</filter>
208 </data>
209 <data format="ps" name="ps_fileB"
210 label="${tool.name} chain in RNA 2 (postscript) on ${on_string}">
211 <filter>'postscript' in outputs</filter>
212 </data>
213 <data format="txt" name="anchors_fasta"
214 label="${tool.name} anchor constraints from chain (fasta) on ${on_string}">
215 <filter>'anchors-fasta' in outputs</filter>
216 </data>
217 <data format="txt" name="anchors_ppA"
218 label="${tool.name} anchors for RNA 1 (pp) on ${on_string}">
219 <filter>'anchors-pp' in outputs</filter>
220 </data>
221 <data format="txt" name="anchors_ppB"
222 label="${tool.name} anchors for RNA 2 (pp) on ${on_string}">
223 <filter>'anchors-pp' in outputs</filter>
224 </data>
225 <data format="clustal" name="clustal"
226 label="${tool.name} chain as alignment (clustal) on ${on_string}">
227 <filter>'clustal' in outputs</filter>
228 </data>
229 <data format="tabular" name="epm_list"
230 label="${tool.name} list of epms on ${on_string}">
231 <filter>'epm_list' in outputs</filter>
232 </data>
233 <data format="tabular" name="chained_epm_list"
234 label="${tool.name} list of epms in chain on ${on_string}">
235 <filter>'chained_epm_list' in outputs</filter>
236 </data>
237 </outputs>
238
239 <tests>
240 <test>
241 <param name="inputA" value="tRNA_2-1.fa" />
242 <param name="inputB" value="tRNA_2-2.fa" />
243 <param name="outputs" value="epm_list" />
244 <output name="epm_list" file="tRNA_2.epms" />
245 </test>
246 </tests>
247
248 <help><![CDATA[ **LocARNA -- Pairwise matching and folding of RNAs (ExpARNA-P)**
249
250 Pairwise matching and folding tool of the LocARNA suite (ExpARNA-P).
251
252 **Input.**
253
254 Input consists of two sequences or alignments, which are specified in
255 fasta, clustal, stockholm, or LocARNA pp format.
256
257 Optionally, one can specify structure and anchor constraints in these
258 input files.b
259
260 **Output.**
261
262 The program enumerates exactly matching local substructures (exact
263 pattern matches = EPMs) and optionally chains them. It returns lists
264 of chained and unchained matches, visualizations of the results and
265 anchor constraints for alignment.
266
267
268 For more information, see
269 .. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
270 ]]></help>
271
272 <expand macro="citations" />
273
274 </tool>