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author devteam
date Fri, 01 Dec 2017 10:24:44 -0500
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1:c9623dbfb799 2:e1f27421adca
1 <tool id="meme_meme" name="MEME" version="1.0.0">
2 <requirements><requirement type='package'>meme</requirement></requirements>
3 <description>- Multiple Em for Motif Elicitation</description>
4 <command>meme "$input1" -o "${html_outfile.files_path}"
5 -nostatus
6
7 ##-p 8 ##number of processors
8
9 #if str( $options_type.options_type_selector ) == 'advanced':
10 -sf "${ str( $options_type.sf ).replace( ' ', '_' ) }"
11 -${options_type.alphabet_type.alphabet_type_selector}
12 -mod "${options_type.mod_type.mod_type_selector}"
13 -nmotifs "${options_type.nmotifs}"
14 -wnsites "${options_type.wnsites}"
15
16 #if $options_type.evt &lt; float('inf'):
17 -evt "${options_type.evt}"
18 #end if
19
20 #if str( $options_type.mod_type.mod_type_selector ) != 'oops':
21 #if str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'nsites':
22 -nsites "${options_type.mod_type.motif_occurrence_type.nsites}"
23 #elif str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'min_max_sites':
24 -minsites "${options_type.mod_type.motif_occurrence_type.minsites}" -maxsites "${options_type.mod_type.motif_occurrence_type.maxsites}"
25 #end if
26 #end if
27
28 #if str( $options_type.motif_width_type.motif_width_type_selector ) == 'exact':
29 -w "${options_type.motif_width_type.width}"
30 #else
31 -minw "${options_type.motif_width_type.minw}" -maxw "${options_type.motif_width_type.maxw}"
32 #end if
33
34 #if str( $options_type.motif_trim_type.motif_trim_type_selector ) == 'nomatrim':
35 -nomatrim
36 #else
37 -wg "${options_type.motif_trim_type.wg}" -ws "${options_type.motif_trim_type.ws}" ${options_type.motif_trim_type.noendgaps}
38 #end if
39
40 #if str( $options_type.bfile ) != 'None':
41 -bfile "${options_type.bfile}"
42 #end if
43
44 #if str( $options_type.pspfile ) != 'None':
45 -psp "${options_type.pspfile}"
46 #end if
47
48 #if str( $options_type.alphabet_type.alphabet_type_selector ) == "dna":
49 ${options_type.alphabet_type.revcomp} ${options_type.alphabet_type.pal}
50 #end if
51
52 -maxiter "${options_type.maxiter}" -distance "${options_type.distance}"
53
54 -prior "${options_type.alphabet_type.prior_type.prior_type_selector}"
55 #if str( $options_type.alphabet_type.prior_type.prior_type_selector ) != 'addone':
56 -b "${options_type.alphabet_type.prior_type.prior_b}"
57 #if str( $options_type.alphabet_type.prior_type.plib ) != 'None':
58 -plib "${options_type.alphabet_type.prior_type.plib}"
59 #end if
60 #end if
61
62 #if str( $options_type.alphabet_type.spmap_type.spmap_type_selector ) == 'cons':
63 -cons "${options_type.alphabet_type.spmap_type.cons}"
64 #else
65 -spmap "${options_type.alphabet_type.spmap_type.spmap_type_selector}"
66 -spfuzz "${options_type.alphabet_type.spmap_type.spfuzz}"
67 #end if
68
69 #if str( $options_type.branching_type.branching_type_selector ) == 'x_branch':
70 -x_branch -bfactor "${options_type.branching_type.bfactor}" -heapsize "${options_type.branching_type.heapsize}"
71 #end if
72
73 ##-maxsize "1000000" ##remove hardcoded maxsize? should increase number of processors instead
74
75 #end if
76
77 2&gt;&amp;1 || echo "Error running MEME."
78
79
80 &amp;&amp; mv ${html_outfile.files_path}/meme.html ${html_outfile}
81
82 &amp;&amp; mv ${html_outfile.files_path}/meme.txt ${txt_outfile}
83
84 &amp;&amp; mv ${html_outfile.files_path}/meme.xml ${xml_outfile}
85
86 </command>
87 <inputs>
88 <param format="fasta" name="input1" type="data" label="Sequences"/>
89
90 <conditional name="options_type">
91 <param name="options_type_selector" type="select" label="Options Configuration">
92 <option value="basic" selected="true">Basic</option>
93 <option value="advanced">Advanced</option>
94 </param>
95 <when value="basic">
96 <!-- do nothing here -->
97 </when>
98 <when value="advanced">
99
100 <param name="sf" type="text" value="Galaxy FASTA Input" label="Name of sequence set" />
101
102 <conditional name="alphabet_type">
103 <param name="alphabet_type_selector" type="select" label="Sequence Alphabet">
104 <option value="protein">Protein</option>
105 <option value="dna" selected="true">DNA</option>
106 </param>
107 <when value="protein">
108 <conditional name="prior_type">
109 <param name="prior_type_selector" type="select" label="Choice of prior">
110 <option value="dirichlet">simple Dirichlet prior</option>
111 <option value="dmix" selected="true">mixture of Dirichlets prior</option>
112 <option value="mega">extremely low variance dmix</option>
113 <option value="megap">mega for all but last iteration of EM; dmix on last iteration</option>
114 <option value="addone">add +1 to each observed count</option>
115 </param>
116 <when value="dirichlet">
117 <param name="prior_b" type="float" value="0.01" label="strength of prior on model parameters" />
118 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
119 </when>
120 <when value="dmix">
121 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" />
122 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
123 </when>
124 <when value="mega">
125 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" />
126 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
127 </when>
128 <when value="megap">
129 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" />
130 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
131 </when>
132 <when value="addone">
133 <!-- no values here? -->
134 </when>
135 </conditional>
136 <conditional name="spmap_type">
137 <param name="spmap_type_selector" type="select" label="EM starting points">
138 <option value="uni">uni</option>
139 <option value="pam" selected="true">pam</option>
140 <option value="cons">Use starting point from string</option>
141 </param>
142 <when value="uni">
143 <param name="spfuzz" type="float" value="0.5" label="Fuzziness of the mapping" />
144 </when>
145 <when value="pam">
146 <param name="spfuzz" type="integer" value="120" label="Fuzziness of the mapping" />
147 </when>
148 <when value="cons">
149 <param name="cons" type="text" value="" label="Starting point from string" />
150 </when>
151 </conditional>
152 </when>
153 <when value="dna">
154 <param name="revcomp" label="Check reverse complement" type="boolean" truevalue="-revcomp" falsevalue="" checked="False"/>
155 <param name="pal" label="Check for palindromes" type="boolean" truevalue="-pal" falsevalue="" checked="False"/>
156 <conditional name="prior_type">
157 <param name="prior_type_selector" type="select" label="Sequence Alphabet">
158 <option value="dirichlet" selected="true">simple Dirichlet prior</option>
159 <option value="dmix">mixture of Dirichlets prior</option>
160 <option value="mega">extremely low variance dmix</option>
161 <option value="megap">mega for all but last iteration of EM; dmix on last iteration</option>
162 <option value="addone">add +1 to each observed count</option>
163 </param>
164 <when value="dirichlet">
165 <param name="prior_b" type="float" value="0.01" label="strength of prior on model parameters" />
166 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
167 </when>
168 <when value="dmix">
169 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" />
170 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
171 </when>
172 <when value="mega">
173 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" />
174 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
175 </when>
176 <when value="megap">
177 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" />
178 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
179 </when>
180 <when value="addone">
181 <!-- no values here? -->
182 </when>
183 </conditional>
184 <conditional name="spmap_type">
185 <param name="spmap_type_selector" type="select" label="EM starting points">
186 <option value="uni" selected="true">uni</option>
187 <option value="pam">pam</option>
188 <option value="cons">Use starting point from string</option>
189 </param>
190 <when value="uni">
191 <param name="spfuzz" type="float" value="0.5" label="Fuzziness of the mapping" />
192 </when>
193 <when value="pam">
194 <param name="spfuzz" type="integer" value="120" label="Fuzziness of the mapping" />
195 </when>
196 <when value="cons">
197 <param name="cons" type="text" value="" label="Starting point from string" />
198 </when>
199 </conditional>
200 </when>
201 </conditional>
202
203 <param name="nmotifs" type="integer" value="1" label="Number of different motifs to search" />
204 <param name="evt" type="float" value="inf" label="E-value to stop looking for motifs" />
205 <conditional name="mod_type">
206 <param name="mod_type_selector" type="select" label="Expected motif distribution">
207 <option value="oops">One Occurrence Per Sequence</option>
208 <option value="zoops" selected="true">Zero or One Occurrence Per Sequence</option>
209 <option value="anr">Any Number of Repetitions</option>
210 </param>
211 <when value="oops">
212 <!-- no values here -->
213 </when>
214 <when value="zoops">
215 <conditional name="motif_occurrence_type">
216 <param name="motif_occurrence_type_selector" type="select" label="Number of motif occurrences">
217 <option value="default" selected="true">Use defaults</option>
218 <option value="nsites">nsites</option>
219 <option value="min_max_sites">min and max sites</option>
220 </param>
221 <when value="default">
222 <!-- no values here -->
223 </when>
224 <when value="nsites">
225 <param name="nsites" type="integer" value="1" label="Search nsites number of occurrences" />
226 </when>
227 <when value="min_max_sites">
228 <param name="minsites" type="integer" value="1" label="minsites" />
229 <param name="maxsites" type="integer" value="50" label="maxsites" />
230 </when>
231 </conditional>
232 </when>
233 <when value="anr">
234 <conditional name="motif_occurrence_type">
235 <param name="motif_occurrence_type_selector" type="select" label="Number of motif occurrences">
236 <option value="default" selected="true">Use defaults</option>
237 <option value="nsites">nsites</option>
238 <option value="min_max_sites">min and max sites</option>
239 </param>
240 <when value="default">
241 <!-- no values here -->
242 </when>
243 <when value="nsites">
244 <param name="nsites" type="integer" value="1" label="Search nsites number of occurrences" />
245 </when>
246 <when value="min_max_sites">
247 <param name="minsites" type="integer" value="1" label="minsites" />
248 <param name="maxsites" type="integer" value="50" label="maxsites" />
249 </when>
250 </conditional>
251 </when>
252 </conditional>
253 <param name="wnsites" type="float" value="0.8" label="Weight on the prior on nsites" />
254
255 <conditional name="motif_width_type">
256 <param name="motif_width_type_selector" type="select" label="Motif width type">
257 <option value="exact">Exact width</option>
258 <option value="range" selected="true">Specify a range</option>
259 </param>
260 <when value="exact">
261 <param name="width" type="integer" value="10" label="Width of motif to search" />
262 </when>
263 <when value="range">
264 <param name="minw" type="integer" value="8" label="Min width of motif to search" />
265 <param name="maxw" type="integer" value="50" label="Max width of motif to search" />
266 </when>
267 </conditional>
268
269 <conditional name="motif_trim_type">
270 <param name="motif_trim_type_selector" type="select" label="Motif trim type">
271 <option value="nomatrim">No motif trim</option>
272 <option value="trim" selected="true">Trim motif</option>
273 </param>
274 <when value="nomatrim">
275 <!-- no values here -->
276 </when>
277 <when value="trim">
278 <param name="wg" type="integer" value="11" label="Gap cost" />
279 <param name="ws" type="integer" value="1" label="Space cost" />
280 <param name="noendgaps" label="Do not penalize endgaps" type="boolean" truevalue="-noendgaps" falsevalue="" checked="False"/>
281 </when>
282 </conditional>
283
284 <param name="bfile" type="data" format="txt" optional="True" label="Background Model" />
285 <param name="pspfile" type="data" format="txt" optional="True" label="Position-Specific Prior" />
286
287 <param name="maxiter" type="integer" value="50" label="Number of iterations of EM to run" />
288 <param name="distance" type="float" value="0.001" label="Convergence criterion" />
289
290 <conditional name="branching_type">
291 <param name="branching_type_selector" type="select" label="x-branching type">
292 <option value="x_branch">Perform x-branching</option>
293 <option value="no_x_branch" selected="true">No x-branching</option>
294 </param>
295 <when value="no_x_branch">
296 <!-- no values here -->
297 </when>
298 <when value="x_branch">
299 <param name="bfactor" type="integer" value="3" label="Number of iterations of branching" />
300 <param name="heapsize" type="integer" value="64" label="Maximum number of heaps to use" />
301 </when>
302 </conditional>
303
304 </when>
305 </conditional>
306
307 <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">
308 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
309 </param>
310
311 </inputs>
312 <outputs>
313 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"/>
314 <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (text)"/>
315 <data format="memexml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)"/>
316 </outputs>
317 <tests>
318 <test>
319 <param name="input1" value="meme/meme/meme_input_1.fasta" ftype="fasta" dbkey="hg19"/>
320 <param name="options_type_selector" value="basic"/>
321 <param name="non_commercial_use" value="True"/>
322 <output name="html_outfile" file="meme/meme/meme_output_html_1.html" lines_diff="12"/>
323 <output name="txt_outfile" file="meme/meme/meme_output_txt_1.txt" lines_diff="12"/>
324 <output name="xml_outfile" file="meme/meme/meme_output_xml_1.xml" lines_diff="8"/>
325 </test>
326 </tests>
327 <help>
328
329 .. class:: warningmark
330
331 **WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted. Before using, be sure to review, agree, and comply with the license.**
332
333 If you want to specify sequence weights, you must include them at the top of your input FASTA file.
334
335 .. class:: infomark
336
337 **To cite MEME:**
338 Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994.
339
340
341 For detailed information on MEME, click here_. To view the license_.
342
343 ------
344
345 **Citation**
346
347 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
348
349 .. _here: http://meme.nbcr.net/meme/meme-intro.html
350 .. _license: http://meme.nbcr.net/meme/COPYRIGHT.html
351
352 </help>
353 </tool>