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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 94c141a71ef115279f1090f782b6f5cdeea9c277
author bgruening
date Mon, 19 Aug 2024 18:53:00 +0000
parents e66514da3a99
children
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2:e66514da3a99 3:a80f279b4ad0
1 <tool id="locarna_exparnap" name="LocARNA Exact Matcher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 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
6 <macros> 5 <macros>
7 <import>macros.xml</import> 6 <import>macros.xml</import>
8 </macros> 7 </macros>
9 8 <expand macro="requirements"/>
10 <expand macro="requirements" /> 9 <expand macro="stdio"/>
11 10 <expand macro="version"/>
12 <expand macro="stdio" />
13
14 <expand macro="version" />
15
16 <command><![CDATA[ 11 <command><![CDATA[
17 exparna_p 12 exparna_p
18
19 '$inputA' 13 '$inputA'
20 '$inputB' 14 '$inputB'
21 15
22 ## -------------------- scoring parameters 16 ## -------------------- scoring parameters -------------#
23 #
24 $Scoring.no_stacking 17 $Scoring.no_stacking
25 --alpha_1 $Scoring.alpha_1 18 --alpha_1 $Scoring.alpha_1
26 --alpha_2 $Scoring.alpha_2 19 --alpha_2 $Scoring.alpha_2
27 --alpha_3 $Scoring.alpha_3 20 --alpha_3 $Scoring.alpha_3
28 --struct-mismatch-score $Scoring.struct_mismatch_score 21 --struct-mismatch-score $Scoring.struct_mismatch_score
33 --prob_unpaired_in_loop_threshold $Heuristics.prob_unpaired_in_loop_threshold 26 --prob_unpaired_in_loop_threshold $Heuristics.prob_unpaired_in_loop_threshold
34 --prob_basepair_in_loop_threshold $Heuristics.prob_basepair_in_loop_threshold 27 --prob_basepair_in_loop_threshold $Heuristics.prob_basepair_in_loop_threshold
35 28
36 @CONSTRAINT_ARGS@ 29 @CONSTRAINT_ARGS@
37 @FOLDING_ARGS@ 30 @FOLDING_ARGS@
38 ## -------------------- other parameters 31 ## -------------------- other parameters---------------- #
39 #
40 #if str($Other.subopt.subopt_selector) == "on" 32 #if str($Other.subopt.subopt_selector) == "on"
41 --diff-to-opt-score $Other.subopt.diff_to_opt_score 33 --diff-to-opt-score $Other.subopt.diff_to_opt_score
42 --number-of-EPMs $Other.subopt.number_of_EPMs 34 --number-of-EPMs $Other.subopt.number_of_EPMs
43 #end if 35 #end if
44 36
47 $Other.inexact_struct_match 39 $Other.inexact_struct_match
48 $Other.add_filter 40 $Other.add_filter
49 $Other.no_chaining 41 $Other.no_chaining
50 --out-min-prob $Other.out_min_prob 42 --out-min-prob $Other.out_min_prob
51 43
52 ## -------------------- output 44 ## -------------------- output ---------------- #
53 45
54 #if 'postscript' in str($outputs).split(",") 46 #if 'postscript' in str($outputs).split(",")
55 --output-ps 47 --output-ps
56 --PS_fileA '$ps_fileA' 48 --PS_fileA '$ps_fileA'
57 --PS_fileB '$ps_fileB' 49 --PS_fileB '$ps_fileB'
77 --output-chained-epm-list '$chained_epm_list' 69 --output-chained-epm-list '$chained_epm_list'
78 #end if 70 #end if
79 71
80 @STDOUT_ARGS@ 72 @STDOUT_ARGS@
81 73
82 ## -------------------- post processing 74 ## -------------------- post processing --------------#
83 75
84 #if 'anchors-pp' in str($outputs).split(",") 76 #if 'anchors-pp' in str($outputs).split(",")
85 && mv anchors_pp_A.pp '$anchors_ppA' 77 && mv anchors_pp_A.pp '$anchors_ppA'
86 && mv anchors_pp_B.pp '$anchors_ppB' 78 && mv anchors_pp_B.pp '$anchors_ppB'
87 #end if 79 #end if
88 80
89 ]]></command> 81 ]]></command>
90 82
91 <inputs> 83 <inputs>
92 <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A" 84 <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A" help="First sequence in fasta, clustal, dp_ps, or PP2.0 format"/>
93 help="First sequence in fasta, clustal, dp_ps, or PP2.0 format" 85 <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B" help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"/>
94 /> 86 <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output options">
95 <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B" 87 <option value="postscript" selected="false">Best EPM chain as colored postscript</option>
96 help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format" 88 <option value="anchors-fasta" selected="false">Fasta with anchor constraints from chaining</option>
97 /> 89 <option value="anchors-pp" selected="false">LocARNA PP files merging input PPs and anchor constraints from chaining</option>
98 90 <option value="clustal" selected="false">Chain as alignment in Clustal format</option>
99 <param name="outputs" type="select" display="checkboxes" multiple="true"
100 label="Output options">
101 <option value="postscript" selected="false">Best EPM chain
102 as colored postscript</option>
103 <option value="anchors-fasta" selected="false">Fasta with anchor
104 constraints from chaining</option>
105 <option value="anchors-pp" selected="false">LocARNA PP
106 files merging input PPs and anchor constraints from
107 chaining</option>
108 <option value="clustal" selected="false">Chain as
109 alignment in Clustal format</option>
110 <option value="epm_list" selected="false">List of the found EPMs</option> 91 <option value="epm_list" selected="false">List of the found EPMs</option>
111 <option value="chained_epm_list" selected="false">List of 92 <option value="chained_epm_list" selected="false">List of EPMs in the best chain</option>
112 EPMs in the best chain</option>
113 </param> 93 </param>
114
115 <param name="stdout_verbosity" type="select" label="Standard output verbosity"> 94 <param name="stdout_verbosity" type="select" label="Standard output verbosity">
116 <option value="--quiet">Don't report standard 95 <option value="--quiet">Don't report standard output</option>
117 output</option>
118 <option value="" selected="true">Non verbose</option> 96 <option value="" selected="true">Non verbose</option>
119 <option value="--verbose">Verbose</option> 97 <option value="--verbose">Verbose</option>
120 </param> 98 </param>
121
122 <section name="Scoring" title="Scoring parameters"> 99 <section name="Scoring" title="Scoring parameters">
123 <param argument="--alpha_1" 100 <param argument="--alpha_1" type="integer" value="1" min="0" max="50" label="Sequence score factor"/>
124 type="integer" value="1" min="0" max="50" 101 <param argument="--alpha_2" type="integer" value="5" min="0" max="50" label="Structure score factor"/>
125 label="Sequence score factor" 102 <param argument="--no-stacking" type="boolean" truevalue="" falsevalue="--no-stacking" label="Add stacking terms"/>
126 /> 103 <param argument="--alpha_3" type="integer" value="5" min="0" max="50" label="Stacking score factor"/>
127 <param argument="--alpha_2" 104 <param argument="--struct-mismatch-score" type="integer" value="-10" min="-100" max="0" label="Score for nucleotide mismatch in base pair match"/>
128 type="integer" value="5" min="0" max="50" 105 </section>
129 label="Structure score factor"
130 />
131 <param argument="--no-stacking" type="boolean"
132 truevalue="" falsevalue="--no-stacking"
133 label="Add stacking terms"
134 />
135 <param argument="--alpha_3"
136 type="integer" value="5" min="0" max="50"
137 label="Stacking score factor"
138 />
139 <param argument="--struct-mismatch-score"
140 type="integer" value="-10" min="-100" max="0"
141 label="Score for nucleotide mismatch in base pair match"
142 />
143 </section>
144
145 <section name="Folding" title="RNA folding parameters"> 106 <section name="Folding" title="RNA folding parameters">
146 <expand macro="common_folding_parameters" /> 107 <expand macro="common_folding_parameters" />
147 </section> 108 </section>
148
149 <section name="Heuristics" title="Heuristic parameters"> 109 <section name="Heuristics" title="Heuristic parameters">
150 <expand macro="common_heuristic_parameters" /> 110 <expand macro="common_heuristic_parameters" />
151 <expand macro="max_diff_parameters" /> 111 <expand macro="max_diff_parameters" />
152 <expand macro="in_loop_ratio_parameters" /> 112 <expand macro="in_loop_ratio_parameters" />
153 <expand macro="exparnap_in_loop_parameters" /> 113 <expand macro="exparnap_in_loop_parameters" />
154 </section> 114 </section>
155
156 <section name="Constraints" title="Constraint parameters"> 115 <section name="Constraints" title="Constraint parameters">
157 <expand macro="common_constraint_parameters" /> 116 <expand macro="common_constraint_parameters" />
158 </section> 117 </section>
159
160
161 <section name="Other" title="Other parameters"> 118 <section name="Other" title="Other parameters">
162 <conditional name="subopt"> 119 <conditional name="subopt">
163 <param name="subopt_selector" type="select" 120 <param name="subopt_selector" type="select" label="Suboptimal traceback of EPMs (exact pattern matches)" help="(--subopt)">
164 label="Suboptimal traceback of EPMs (exact pattern matches)" 121 <option value="off">Enumerate only optimal EPMs</option>
165 help="(--subopt)">
166 <option value="off">Enumerate only optimal
167 EPMs</option>
168 <option value="on">Perform suboptimal traceback of EPMs</option> 122 <option value="on">Perform suboptimal traceback of EPMs</option>
169 </param> 123 </param>
170 <when value="off" /> 124 <when value="off" />
171 <when value="on"> 125 <when value="on">
172 <param argument="--diff-to-opt-score" 126 <param argument="--diff-to-opt-score" type="integer" value="-1" min="-20" max="0" label="Maximum score difference to optimum" />
173 type="integer" value="-1" min="-20" max="0" 127 <param argument="--number-of-EPMs" type="integer" value="100" min="1" max="10000" label="Maximal number of EPMs" />
174 label="Maximum score difference to optimum" />
175 <param argument="--number-of-EPMs"
176 type="integer" value="100" min="1" max="10000"
177 label="Maximal number of EPMs" />
178 </when> 128 </when>
179 </conditional> 129 </conditional>
180 130
181 <param argument="--min-score" 131 <param argument="--min-score" type="integer" value="30" min="0" max="1000" label="Minimum score of EPM" />
182 type="integer" value="30" min="0" max="1000" 132 <param argument="--inexact-struct-match" type="boolean" truevalue="--inexact-struct-match" falsevalue="" label="Allow inexact structure matches"/>
183 label="Minimum score of EPM" /> 133 <param argument="--add-filter" type="boolean" truevalue="--add-filter" falsevalue="" checked="false" label="Apply an additional filter to enumerate only EPMs that are maximally extended (only inexact)"/>
184 134 <param argument="--no-chaining" type="boolean" truevalue="" falsevalue="--no-chaining" checked="true" label="Find best overall chain by chaining"/>
185 <param argument="--inexact-struct-match" type="boolean" 135 <param argument="--out-min-prob" type="float" value="0.0005" min="0" max="1" label="Minimal probability in output (min-prob overrides if smaller)"/>
186 truevalue="--inexact-struct-match" falsevalue=""
187 label="Allow inexact structure matches"/>
188
189 <param argument="--add-filter" type="boolean"
190 truevalue="--add-filter" falsevalue="" checked="false"
191 label="Apply an additional filter to enumerate only
192 EPMs that are maximally extended (only inexact)"/>
193
194 <param argument="--no-chaining" type="boolean"
195 truevalue="" falsevalue="--no-chaining" checked="true"
196 label="Find best overall chain by chaining"/>
197
198 <param argument="--out-min-prob"
199 type="float" value="0.0005" min="0" max="1"
200 label="Minimal probability in output (min-prob overrides if smaller)"/>
201
202 </section> 136 </section>
203 </inputs> 137 </inputs>
204 138
205 <outputs> 139 <outputs>
206 <expand macro="standard_outupt" /> 140 <expand macro="standard_outupt" />
207 <data format="ps" name="ps_fileA" 141 <data format="ps" name="ps_fileA" label="${tool.name} on ${on_string}: chain in RNA 1 (postscript)">
208 label="${tool.name} on ${on_string}: chain in RNA 1 (postscript)">
209 <filter>'postscript' in outputs</filter> 142 <filter>'postscript' in outputs</filter>
210 </data> 143 </data>
211 <data format="ps" name="ps_fileB" 144 <data format="ps" name="ps_fileB" label="${tool.name} on ${on_string}: chain in RNA 2 (postscript)">
212 label="${tool.name} on ${on_string}: chain in RNA 2 (postscript)">
213 <filter>'postscript' in outputs</filter> 145 <filter>'postscript' in outputs</filter>
214 </data> 146 </data>
215 <data format="txt" name="anchors_fasta" 147 <data format="txt" name="anchors_fasta" label="${tool.name} on ${on_string}: anchor constraints from chain (fasta)">
216 label="${tool.name} on ${on_string}: anchor constraints from chain (fasta)">
217 <filter>'anchors-fasta' in outputs</filter> 148 <filter>'anchors-fasta' in outputs</filter>
218 </data> 149 </data>
219 <data format="txt" name="anchors_ppA" 150 <data format="txt" name="anchors_ppA" label="${tool.name} on ${on_string}: anchors for RNA 1 (pp)">
220 label="${tool.name} on ${on_string}: anchors for RNA 1 (pp)">
221 <filter>'anchors-pp' in outputs</filter> 151 <filter>'anchors-pp' in outputs</filter>
222 </data> 152 </data>
223 <data format="txt" name="anchors_ppB" 153 <data format="txt" name="anchors_ppB" label="${tool.name} on ${on_string}: anchors for RNA 2 (pp)">
224 label="${tool.name} on ${on_string}: anchors for RNA 2 (pp)">
225 <filter>'anchors-pp' in outputs</filter> 154 <filter>'anchors-pp' in outputs</filter>
226 </data> 155 </data>
227 <data format="clustal" name="clustal" 156 <data format="clustal" name="clustal" label="${tool.name} on ${on_string}: chain as alignment (clustal)">
228 label="${tool.name} on ${on_string}: chain as alignment (clustal)">
229 <filter>'clustal' in outputs</filter> 157 <filter>'clustal' in outputs</filter>
230 </data> 158 </data>
231 <data format="tabular" name="epm_list" 159 <data format="tabular" name="epm_list" label="${tool.name} on ${on_string}: list of epms">
232 label="${tool.name} on ${on_string}: list of epms">
233 <filter>'epm_list' in outputs</filter> 160 <filter>'epm_list' in outputs</filter>
234 </data> 161 </data>
235 <data format="tabular" name="chained_epm_list" 162 <data format="tabular" name="chained_epm_list" label="${tool.name} on ${on_string}: list of epms in chain">
236 label="${tool.name} on ${on_string}: list of epms in chain">
237 <filter>'chained_epm_list' in outputs</filter> 163 <filter>'chained_epm_list' in outputs</filter>
238 </data> 164 </data>
239 </outputs> 165 </outputs>
240 166
241 <tests> 167 <tests>
242 <test expect_num_outputs="2"> 168 <test expect_num_outputs="2">
243 <param name="inputA" value="tRNA_2-1.fa" /> 169 <param name="inputA" value="tRNA_2-1.fa"/>
244 <param name="inputB" value="tRNA_2-2.fa" /> 170 <param name="inputB" value="tRNA_2-2.fa"/>
245 <param name="outputs" value="epm_list" /> 171 <param name="outputs" value="epm_list"/>
246 <output name="epm_list" file="tRNA_2.epms" /> 172 <output name="epm_list" file="tRNA_2.epms"/>
247 <output name="stdout"> 173 <output name="stdout">
248 <assert_contents> 174 <assert_contents>
249 <has_text text="LCSEPM preprocessing..."/> 175 <has_text text="LCSEPM preprocessing..."/>
250 <has_text text="#EPMs:"/> 176 <has_text text="#EPMs:"/>
251 </assert_contents> 177 </assert_contents>