Mercurial > repos > rnateam > locarna_exparnap
comparison locarna_exparnap.xml @ 0:e91e4f48875e draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
author | rnateam |
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date | Fri, 13 Jan 2017 16:49:16 -0500 (2017-01-13) |
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children | e66514da3a99 |
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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> |