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comparison locarna_exparnap.xml @ 2:e66514da3a99 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 10ccc47885ce71e602d66e157bd475f1facbd042
author bgruening
date Mon, 05 Dec 2022 13:58:16 +0000
parents e91e4f48875e
children a80f279b4ad0
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1:8723e3f8e422 2:e66514da3a99
1 <tool id="locarna_exparnap" name="LocARNA Exact Matcher" version="@VERSION@.0"> 1 <tool id="locarna_exparnap" name="LocARNA Exact Matcher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description> 2 <description>
3 Pairwise Simultaneous Matching and Folding of RNAs (ExpaRNA-P) 3 Pairwise Simultaneous Matching and Folding of RNAs (ExpaRNA-P)
4 </description> 4 </description>
5 5
6 <macros> 6 <macros>
26 --alpha_2 $Scoring.alpha_2 26 --alpha_2 $Scoring.alpha_2
27 --alpha_3 $Scoring.alpha_3 27 --alpha_3 $Scoring.alpha_3
28 --struct-mismatch-score $Scoring.struct_mismatch_score 28 --struct-mismatch-score $Scoring.struct_mismatch_score
29 29
30 @HEURISTIC_ARGS@ 30 @HEURISTIC_ARGS@
31 --max-uil-length-ratio $Heuristics.max_uil_length_ratio
32 --max-bpil-length-ratio $Heuristics.max_bpil_length_ratio
31 --prob_unpaired_in_loop_threshold $Heuristics.prob_unpaired_in_loop_threshold 33 --prob_unpaired_in_loop_threshold $Heuristics.prob_unpaired_in_loop_threshold
32 --prob_basepair_in_loop_threshold $Heuristics.prob_basepair_in_loop_threshold 34 --prob_basepair_in_loop_threshold $Heuristics.prob_basepair_in_loop_threshold
33 35
34 @CONSTRAINT_ARGS@ 36 @CONSTRAINT_ARGS@
35 37 @FOLDING_ARGS@
36 ## -------------------- other parameters 38 ## -------------------- other parameters
37 # 39 #
38 #if str($Other.subopt.subopt_selector) == "on" 40 #if str($Other.subopt.subopt_selector) == "on"
39 --diff-to-opt-score $Other.subopt.diff_to_opt_score 41 --diff-to-opt-score $Other.subopt.diff_to_opt_score
40 --number-of-EPMs $Other.subopt.number_of_EPMs 42 --number-of-EPMs $Other.subopt.number_of_EPMs
92 /> 94 />
93 <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B" 95 <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" 96 help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"
95 /> 97 />
96 98
97 <param name="outputs" type="select" display="checkboxes" multiple="True" 99 <param name="outputs" type="select" display="checkboxes" multiple="true"
98 label="Output options"> 100 label="Output options">
99 <option value="postscript" selected="False">Best EPM chain 101 <option value="postscript" selected="false">Best EPM chain
100 as colored postscript</option> 102 as colored postscript</option>
101 <option value="anchors-fasta" selected="False">Fasta with anchor 103 <option value="anchors-fasta" selected="false">Fasta with anchor
102 constraints from chaining</option> 104 constraints from chaining</option>
103 <option value="anchors-pp" selected="False">LocARNA PP 105 <option value="anchors-pp" selected="false">LocARNA PP
104 files merging input PPs and anchor constraints from 106 files merging input PPs and anchor constraints from
105 chaining</option> 107 chaining</option>
106 <option value="clustal" selected="False">Chain as 108 <option value="clustal" selected="false">Chain as
107 alignment in Clustal format</option> 109 alignment in Clustal format</option>
108 <option value="epm_list" selected="False">List of the found EPMs</option> 110 <option value="epm_list" selected="false">List of the found EPMs</option>
109 <option value="chained_epm_list" selected="False">List of 111 <option value="chained_epm_list" selected="false">List of
110 EPMs in the best chain</option> 112 EPMs in the best chain</option>
111 </param> 113 </param>
112 114
113 <param name="stdout_verbosity" type="select" label="Standard output verbosity"> 115 <param name="stdout_verbosity" type="select" label="Standard output verbosity">
114 <option value="--quiet">Don't report standard 116 <option value="--quiet">Don't report standard
115 output</option> 117 output</option>
116 <option value="" selected="True">Non verbose</option> 118 <option value="" selected="true">Non verbose</option>
117 <option value="--verbose">Verbose</option> 119 <option value="--verbose">Verbose</option>
118 </param> 120 </param>
119 121
120 <section name="Scoring" title="Scoring parameters"> 122 <section name="Scoring" title="Scoring parameters">
121 <param argument="alpha_1" 123 <param argument="--alpha_1"
122 type="integer" value="1" min="0" max="50" 124 type="integer" value="1" min="0" max="50"
123 label="Sequence score factor" 125 label="Sequence score factor"
124 /> 126 />
125 <param argument="alpha_2" 127 <param argument="--alpha_2"
126 type="integer" value="5" min="0" max="50" 128 type="integer" value="5" min="0" max="50"
127 label="Structure score factor" 129 label="Structure score factor"
128 /> 130 />
129 <param name="no_stacking" argument="no-stacking" type="boolean" 131 <param argument="--no-stacking" type="boolean"
130 truevalue="" falsevalue="--no-stacking" 132 truevalue="" falsevalue="--no-stacking"
131 label="Add stacking terms" 133 label="Add stacking terms"
132 /> 134 />
133 <param argument="alpha_3" 135 <param argument="--alpha_3"
134 type="integer" value="5" min="0" max="50" 136 type="integer" value="5" min="0" max="50"
135 label="Stacking score factor" 137 label="Stacking score factor"
136 /> 138 />
137 <param name="struct_mismatch_score" argument="struct-mismatch-score" 139 <param argument="--struct-mismatch-score"
138 type="integer" value="-10" min="-100" max="0" 140 type="integer" value="-10" min="-100" max="0"
139 label="Score for nucleotide mismatch in base pair match" 141 label="Score for nucleotide mismatch in base pair match"
140 /> 142 />
141 </section> 143 </section>
142 144
165 EPMs</option> 167 EPMs</option>
166 <option value="on">Perform suboptimal traceback of EPMs</option> 168 <option value="on">Perform suboptimal traceback of EPMs</option>
167 </param> 169 </param>
168 <when value="off" /> 170 <when value="off" />
169 <when value="on"> 171 <when value="on">
170 <param name="diff_to_opt_score" argument="diff-to-opt-score" 172 <param argument="--diff-to-opt-score"
171 type="integer" value="-1" min="-20" max="0" 173 type="integer" value="-1" min="-20" max="0"
172 label="Maximum score difference to optimum" /> 174 label="Maximum score difference to optimum" />
173 <param name="number_of_EPMs" argument="number-of-EPMs" 175 <param argument="--number-of-EPMs"
174 type="integer" value="100" min="1" max="10000" 176 type="integer" value="100" min="1" max="10000"
175 label="Maximal number of EPMs" /> 177 label="Maximal number of EPMs" />
176 </when> 178 </when>
177 </conditional> 179 </conditional>
178 180
179 <param name="min_score" argument="min-score" 181 <param argument="--min-score"
180 type="integer" value="30" min="0" max="1000" 182 type="integer" value="30" min="0" max="1000"
181 label="Minimum score of EPM" /> 183 label="Minimum score of EPM" />
182 184
183 <param name="inexact_struct_match" argument="inexact-struct-match" type="boolean" 185 <param argument="--inexact-struct-match" type="boolean"
184 truevalue="--inexact-struct-match" falsevalue="" 186 truevalue="--inexact-struct-match" falsevalue=""
185 label="Allow inexact structure matches"/> 187 label="Allow inexact structure matches"/>
186 188
187 <param name="add_filter" argument="add-filter" type="boolean" 189 <param argument="--add-filter" type="boolean"
188 truevalue="--add-filter" falsevalue="" checked="False" 190 truevalue="--add-filter" falsevalue="" checked="false"
189 label="Apply an additional filter to enumerate only 191 label="Apply an additional filter to enumerate only
190 EPMs that are maximally extended (only inexact)"/> 192 EPMs that are maximally extended (only inexact)"/>
191 193
192 <param name="no_chaining" argument="no-chaining" type="boolean" 194 <param argument="--no-chaining" type="boolean"
193 truevalue="" falsevalue="--no-chaining" checked="True" 195 truevalue="" falsevalue="--no-chaining" checked="true"
194 label="Find best overall chain by chaining"/> 196 label="Find best overall chain by chaining"/>
195 197
196 <param name="out_min_prob" argument="out-min-prob" 198 <param argument="--out-min-prob"
197 type="float" value="0.0005" min="0" max="1" 199 type="float" value="0.0005" min="0" max="1"
198 label="Minimal probability in output (min-prob overrides if smaller)"/> 200 label="Minimal probability in output (min-prob overrides if smaller)"/>
199 201
200 </section> 202 </section>
201 </inputs> 203 </inputs>
202 204
203 <outputs> 205 <outputs>
204 <expand macro="standard_outupt" /> 206 <expand macro="standard_outupt" />
205 <data format="ps" name="ps_fileA" 207 <data format="ps" name="ps_fileA"
206 label="${tool.name} chain in RNA 1 (postscript) on ${on_string}"> 208 label="${tool.name} on ${on_string}: chain in RNA 1 (postscript)">
207 <filter>'postscript' in outputs</filter> 209 <filter>'postscript' in outputs</filter>
208 </data> 210 </data>
209 <data format="ps" name="ps_fileB" 211 <data format="ps" name="ps_fileB"
210 label="${tool.name} chain in RNA 2 (postscript) on ${on_string}"> 212 label="${tool.name} on ${on_string}: chain in RNA 2 (postscript)">
211 <filter>'postscript' in outputs</filter> 213 <filter>'postscript' in outputs</filter>
212 </data> 214 </data>
213 <data format="txt" name="anchors_fasta" 215 <data format="txt" name="anchors_fasta"
214 label="${tool.name} anchor constraints from chain (fasta) on ${on_string}"> 216 label="${tool.name} on ${on_string}: anchor constraints from chain (fasta)">
215 <filter>'anchors-fasta' in outputs</filter> 217 <filter>'anchors-fasta' in outputs</filter>
216 </data> 218 </data>
217 <data format="txt" name="anchors_ppA" 219 <data format="txt" name="anchors_ppA"
218 label="${tool.name} anchors for RNA 1 (pp) on ${on_string}"> 220 label="${tool.name} on ${on_string}: anchors for RNA 1 (pp)">
219 <filter>'anchors-pp' in outputs</filter> 221 <filter>'anchors-pp' in outputs</filter>
220 </data> 222 </data>
221 <data format="txt" name="anchors_ppB" 223 <data format="txt" name="anchors_ppB"
222 label="${tool.name} anchors for RNA 2 (pp) on ${on_string}"> 224 label="${tool.name} on ${on_string}: anchors for RNA 2 (pp)">
223 <filter>'anchors-pp' in outputs</filter> 225 <filter>'anchors-pp' in outputs</filter>
224 </data> 226 </data>
225 <data format="clustal" name="clustal" 227 <data format="clustal" name="clustal"
226 label="${tool.name} chain as alignment (clustal) on ${on_string}"> 228 label="${tool.name} on ${on_string}: chain as alignment (clustal)">
227 <filter>'clustal' in outputs</filter> 229 <filter>'clustal' in outputs</filter>
228 </data> 230 </data>
229 <data format="tabular" name="epm_list" 231 <data format="tabular" name="epm_list"
230 label="${tool.name} list of epms on ${on_string}"> 232 label="${tool.name} on ${on_string}: list of epms">
231 <filter>'epm_list' in outputs</filter> 233 <filter>'epm_list' in outputs</filter>
232 </data> 234 </data>
233 <data format="tabular" name="chained_epm_list" 235 <data format="tabular" name="chained_epm_list"
234 label="${tool.name} list of epms in chain on ${on_string}"> 236 label="${tool.name} on ${on_string}: list of epms in chain">
235 <filter>'chained_epm_list' in outputs</filter> 237 <filter>'chained_epm_list' in outputs</filter>
236 </data> 238 </data>
237 </outputs> 239 </outputs>
238 240
239 <tests> 241 <tests>
240 <test> 242 <test expect_num_outputs="2">
241 <param name="inputA" value="tRNA_2-1.fa" /> 243 <param name="inputA" value="tRNA_2-1.fa" />
242 <param name="inputB" value="tRNA_2-2.fa" /> 244 <param name="inputB" value="tRNA_2-2.fa" />
243 <param name="outputs" value="epm_list" /> 245 <param name="outputs" value="epm_list" />
244 <output name="epm_list" file="tRNA_2.epms" /> 246 <output name="epm_list" file="tRNA_2.epms" />
247 <output name="stdout">
248 <assert_contents>
249 <has_text text="LCSEPM preprocessing..."/>
250 <has_text text="#EPMs:"/>
251 </assert_contents>
252 </output>
245 </test> 253 </test>
246 </tests> 254 </tests>
247 255
248 <help><![CDATA[ **LocARNA -- Pairwise matching and folding of RNAs (ExpARNA-P)** 256 <help><![CDATA[ **LocARNA -- Pairwise matching and folding of RNAs (ExpARNA-P)**
249 257