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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
author iuc
date Wed, 27 Nov 2024 13:22:18 +0000
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1 <tool id="sfold" name="Sfold" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Prediction of RNA secondary structures through structure ensemble sampling</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <requirements>
7 <expand macro="requirements"/>
8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[
10 #if not $non_commercial_use
11 >&2 echo "this tool is only available for non commercial use";
12 exit 1;
13 #end if
14 mkdir -p 'output' &&
15 sfold '$fasta'
16 -a $a
17 #if $f:
18 -f '$f'
19 #end if
20 #if str($l) != '':
21 -l $l
22 #end if
23 #if $m:
24 -m '$m'
25 #end if
26 -w $w
27 -i $i
28 ]]></command>
29 <inputs>
30 <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False">
31 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
32 </param>
33 <param argument="fasta" type="data" format="fasta" label="FASTA input"/>
34 <param argument="-a" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Run clustering on the sampled ensemble?"/>
35 <param argument="-f" type="data" format="ct" optional="true" label="Constrain data" help="Constraint syntax follows what is used in mfold 3.1"/>
36 <param argument="-l" type="integer" min="0" optional="true" label="Maximum distance between paired bases"/>
37 <param argument="-m" type="data" format="ct" optional="true" label="MFE structure" help="If provided, Sfold clustering module will determine the cluster to which this structure belongs."/>
38 <param argument="-w" type="integer" value="20" label="Length of antisense oligos"/>
39 <param argument="-i" type="select" label="Module">
40 <option value="0">None</option>
41 <option value="1">Sirna</option>
42 <option value="2">Soligo</option>
43 <option value="3">Both</option>
44 </param>
45 <param name="output_selector" type="select" multiple="true" optional="true" display="checkboxes" label="Output options">
46 <option value="ct" selected="true">Output ct files</option>
47 <option value="bp" selected="true">Output bp files</option>
48 <option value="clusters">Output cluster files</option>
49 </param>
50 </inputs>
51 <outputs>
52 <collection name="sfold_out" type="list" label="${tool.name} on ${on_string}: sfold log files">
53 <discover_datasets pattern="(?P&lt;name&gt;.+)\.out$" format="txt" directory="output/"/>
54 </collection>
55 <collection name="sfold_bp" type="list" label="${tool.name} on ${on_string}: sfold bp files">
56 <discover_datasets pattern="(?P&lt;name&gt;.+)\.bp$" format="txt" directory="output/"/>
57 <filter>'bp' in output_selector</filter>
58 </collection>
59 <collection name="sfold_ct" type="list" label="${tool.name} on ${on_string}: sfold ct files">
60 <discover_datasets pattern="(?P&lt;name&gt;.+)\.ct$" format="ct" directory="output/"/>
61 <filter>'ct' in output_selector</filter>
62 </collection>
63 <collection name="sfold_cluster_out" type="list" label="${tool.name} on ${on_string}: sfold cluster log files">
64 <discover_datasets pattern="(?P&lt;name&gt;.+)\.out$" format="txt" directory="output/clusters"/>
65 <discover_datasets pattern="(?P&lt;name&gt;.+)\.list$" format="txt" directory="output/clusters"/>
66 <filter>'clusters' in output_selector</filter>
67 </collection>
68 <collection name="sfold_cluster_bp" type="list" label="${tool.name} on ${on_string}: sfold cluster bp files">
69 <discover_datasets pattern="(?P&lt;name&gt;.+)\.bp$" format="txt" directory="output/clusters"/>
70 <filter>'clusters' in output_selector and 'bp' in output_selector</filter>
71 </collection>
72 <collection name="sfold_cluster_ct" type="list" label="${tool.name} on ${on_string}: sfold cluster ct files">
73 <discover_datasets pattern="(?P&lt;name&gt;.+)\.ct$" format="ct" directory="output/clusters"/>
74 <filter>'clusters' in output_selector and 'ct' in output_selector</filter>
75 </collection>
76 </outputs>
77 <tests>
78 <test expect_num_outputs="6">
79 <param name="non_commercial_use" value="true"/>
80 <param name="fasta" value="seq.fasta"/>
81 <param name="a" value="true"/>
82 <param name="f" value="cons.ct"/>
83 <param name="l" value="30"/>
84 <param name="m" value="mfe.ct"/>
85 <param name="w" value="20"/>
86 <param name="i" value="1"/>
87 <param name="output_selector" value="ct,bp,clusters"/>
88 <output_collection name="sfold_out" type="list">
89 <element name="10structure">
90 <assert_contents>
91 <has_n_lines n="770"/>
92 <has_text text="Structure 1 -28.90 0.74863E-01"/>
93 </assert_contents>
94 </element>
95 <element name="10structure_2">
96 <assert_contents>
97 <has_n_lines n="10"/>
98 </assert_contents>
99 </element>
100 <element name="bp.dist.from.ecentroid">
101 <assert_contents>
102 <has_n_lines n="1001"/>
103 <has_text text="1 5"/>
104 </assert_contents>
105 </element>
106 <element name="bp">
107 <assert_contents>
108 <has_text text="Structure 1"/>
109 </assert_contents>
110 </element>
111 <element name="bprob">
112 <assert_contents>
113 <has_n_lines n="4"/>
114 <has_text text=".16225072123690604808E+01L"/>
115 </assert_contents>
116 </element>
117 <element name="cdf">
118 <assert_contents>
119 <has_n_lines n="101"/>
120 </assert_contents>
121 </element>
122 <element name="fe">
123 <assert_contents>
124 <has_n_lines n="1000"/>
125 <has_text text="1 -28.70"/>
126 </assert_contents>
127 </element>
128 <element name="fe_init">
129 <assert_contents>
130 <has_n_lines n="1002"/>
131 <has_text text="Ensemble free energy (based on initial energies):-RT ln(U)= -28.297589224477537 "/>
132 </assert_contents>
133 </element>
134 <element name="loopr">
135 <assert_contents>
136 <has_n_lines n="76"/>
137 </assert_contents>
138 </element>
139 <element name="pdf">
140 <assert_contents>
141 <has_n_lines n="21"/>
142 </assert_contents>
143 </element>
144 <element name="sample">
145 <assert_contents>
146 <has_n_lines n="1"/>
147 <has_text text="Structure data in BP format removed to"/>
148 </assert_contents>
149 </element>
150 <element name="sample_1000">
151 <assert_contents>
152 <has_text text="(i j k): helix formed by base pairs i-j, (i+1)-(j-1),...,(i+k-1)-(j-k+1)"/>
153 </assert_contents>
154 </element>
155 <element name="sclass">
156 <assert_contents>
157 <has_text text="Sequence length = 76"/>
158 </assert_contents>
159 </element>
160 <element name="sfold">
161 <assert_contents>
162 <has_n_lines n="42"/>
163 <has_text text="1 G"/>
164 </assert_contents>
165 </element>
166 <element name="smfe">
167 <assert_contents>
168 <has_n_lines n="2"/>
169 <has_text text="Minimum free energy in the sample (SMFE)= -28.90 kcal/mol"/>
170 </assert_contents>
171 </element>
172 <element name="sstrand">
173 <assert_contents>
174 <has_n_lines n="76"/>
175 </assert_contents>
176 </element>
177 </output_collection>
178 <output_collection name="sfold_bp" type="list">
179 <element name="ecentroid">
180 <assert_contents>
181 <has_text text="1 72"/>
182 </assert_contents>
183 </element>
184 </output_collection>
185 <output_collection name="sfold_ct" type="list">
186 <element name="ecentroid">
187 <assert_contents>
188 <has_n_lines n="78"/>
189 </assert_contents>
190 </element>
191 </output_collection>
192 <output_collection name="sfold_cluster_out" type="list">
193 <element name="c01.2dhist">
194 <assert_contents>
195 <has_text text="1"/>
196 </assert_contents>
197 </element>
198 <element name="c01.bp.dist.from.ccentroid">
199 <assert_contents>
200 <has_text text="1"/>
201 </assert_contents>
202 </element>
203 <element name="c01.bp">
204 <assert_contents>
205 <has_text text="Structure 1"/>
206 </assert_contents>
207 </element>
208 <element name="c01.fe">
209 <assert_contents>
210 <has_text text=" 1"/>
211 </assert_contents>
212 </element>
213 <element name="c02.2dhist">
214 <assert_contents>
215 <has_text text="72"/>
216 </assert_contents>
217 </element>
218 <element name="c02.bp.dist.from.ccentroid">
219 <assert_contents>
220 <has_text text="1"/>
221 </assert_contents>
222 </element>
223 <element name="c02.bp">
224 <assert_contents>
225 <has_text text="Structure 1"/>
226 </assert_contents>
227 </element>
228 <element name="c02.fe">
229 <assert_contents>
230 <has_text text="10"/>
231 </assert_contents>
232 </element>
233 <element name="ch.index">
234 <assert_contents>
235 <has_n_lines n="19"/>
236 </assert_contents>
237 </element>
238 </output_collection>
239 <output_collection name="sfold_cluster_bp" type="list">
240 <element name="c01.ccentroid">
241 <assert_contents>
242 <has_text text="1 72"/>
243 </assert_contents>
244 </element>
245 <element name="c02.ccentroid">
246 <assert_contents>
247 <has_text text="Structure 1"/>
248 </assert_contents>
249 </element>
250 </output_collection>
251 <output_collection name="sfold_cluster_ct" type="list">
252 <element name="c01.ccentroid">
253 <assert_contents>
254 <has_n_lines n="78"/>
255 <has_text text="Length: 76"/>
256 </assert_contents>
257 </element>
258 <element name="c02.ccentroid">
259 <assert_contents>
260 <has_n_lines n="78"/>
261 <has_text text="Length: 76"/>
262 </assert_contents>
263 </element>
264 </output_collection>
265 </test>
266 <test expect_num_outputs="4">
267 <param name="non_commercial_use" value="true"/>
268 <param name="fasta" value="seq.fasta"/>
269 <param name="a" value="true"/>
270 <param name="f" value="cons.ct"/>
271 <param name="l" value="30"/>
272 <param name="m" value="mfe.ct"/>
273 <param name="w" value="20"/>
274 <param name="i" value="1"/>
275 <param name="output_selector" value="bp,clusters"/>
276 <output_collection name="sfold_cluster_bp" type="list">
277 <element name="c01.ccentroid">
278 <assert_contents>
279 <has_text text="1 72"/>
280 </assert_contents>
281 </element>
282 <element name="c02.ccentroid">
283 <assert_contents>
284 <has_text text="Structure 1"/>
285 </assert_contents>
286 </element>
287 </output_collection>
288 <output_collection name="sfold_bp" type="list">
289 <element name="ecentroid">
290 <assert_contents>
291 <has_text text="1 72"/>
292 </assert_contents>
293 </element>
294 </output_collection>
295 </test>
296 </tests>
297 <help><![CDATA[
298 Sfold is a software package for statistical folding and rational design of nucleic acids.
299
300 It provides tools for predicting RNA secondary structures, designing antisense oligonucleotides, and analyzing RNA folding patterns. Sfold is widely used in academic research for studying
301 RNA structure and function.
302
303 Input Format
304
305 -----------
306
307 The program requires one input file of RNA sequence in FASTA format.
308
309 Sfold options
310
311 ------------
312
313 The program can run based on the clustering on the sampled ensemble or not.
314 It can also predict the secondary structure based on the constraint and MFE structure files.
315 The sfold has two different modules:
316
317 * SiRNA : Target accessibility prediction and RNA duplex thermodynamics for rational siRNA design
318 * Solig: Target accessibility prediction and rational design of antisense oligonucleotides and nucleic acid probes
319
320 The program can be run based on the above-mentioned modules, both of them or none of them.
321
322 Output Files
323
324 ------------
325
326 The Sfold program generates 4 different types of output files. sfold.out and sclass.out in your output log files, save the general messages from standard output/error from which you can know if your Sfold run was successful. Most of the other
327 files contain a header section that defines the formats and meanings of the data in the output.
328
329 ------------
330
331 Important: The program usage is restricted to non-commercial and academic research.
332 ]]>
333 </help>
334 <expand macro="citations" />
335 </tool>