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comparison meme.xml @ 4:e5e9a09ac2de draft

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author iuc
date Wed, 29 Jun 2016 08:26:51 -0400
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3:d44c2896957f 4:e5e9a09ac2de
1 <tool id="meme_meme" name="MEME" version="4.11.0.1">
2 <description>- Multiple Em for Motif Elicitation</description>
3 <requirements>
4 <requirement type="package" version="6.9.3">imagemagick</requirement>
5 <requirement type="package" version="4.11.0">meme</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 meme "$input1"
10 -o "${html_outfile.files_path}"
11 -nostatus
12 -maxsize 1000000
13 #if str( $options_type.options_type_selector ) == 'advanced':
14 -sf "${ str( $options_type.sf ).replace( ' ', '_' ) }"
15 -${options_type.alphabet_type.alphabet_type_selector}
16 -mod "${options_type.mod_type.mod_type_selector}"
17 -nmotifs "${options_type.nmotifs}"
18 -wnsites "${options_type.wnsites}"
19 #if $options_type.evt < float('inf'):
20 -evt "${options_type.evt}"
21 #end if
22 #if str( $options_type.mod_type.mod_type_selector ) != 'oops':
23 #if str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'nsites':
24 -nsites "${options_type.mod_type.motif_occurrence_type.nsites}"
25 #elif str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'min_max_sites':
26 -minsites "${options_type.mod_type.motif_occurrence_type.minsites}"
27 -maxsites "${options_type.mod_type.motif_occurrence_type.maxsites}"
28 #end if
29 #end if
30 #if str( $options_type.motif_width_type.motif_width_type_selector ) == 'exact':
31 -w "${options_type.motif_width_type.width}"
32 #else
33 -minw "${options_type.motif_width_type.minw}"
34 -maxw "${options_type.motif_width_type.maxw}"
35 #end if
36 #if str( $options_type.motif_trim_type.motif_trim_type_selector ) == 'nomatrim':
37 -nomatrim
38 #else
39 -wg "${options_type.motif_trim_type.wg}"
40 -ws "${options_type.motif_trim_type.ws}"
41 ${options_type.motif_trim_type.noendgaps}
42 #end if
43 #if str( $options_type.bfile ) != 'None':
44 -bfile "${options_type.bfile}"
45 #end if
46 #if str( $options_type.pspfile ) != 'None':
47 -psp "${options_type.pspfile}"
48 #end if
49 #if str( $options_type.alphabet_type.alphabet_type_selector ) == "dna":
50 ${options_type.alphabet_type.revcomp} ${options_type.alphabet_type.pal}
51 #end if
52 -maxiter "${options_type.maxiter}"
53 -distance "${options_type.distance}"
54 -prior "${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 #if str( $options_type.alphabet_type.spmap_type.spmap_type_selector ) == 'cons':
62 -cons "${options_type.alphabet_type.spmap_type.cons}"
63 #else
64 -spmap "${options_type.alphabet_type.spmap_type.spmap_type_selector}"
65 -spfuzz "${options_type.alphabet_type.spmap_type.spfuzz}"
66 #end if
67 #if str( $options_type.branching_type.branching_type_selector ) == 'x_branch':
68 -x_branch
69 -bfactor "${options_type.branching_type.bfactor}"
70 -heapsize "${options_type.branching_type.heapsize}"
71 #end if
72 #end if
73 2>&1 || echo "Error running MEME."
74 && mv ${html_outfile.files_path}/meme.html ${html_outfile}
75 && mv ${html_outfile.files_path}/meme.txt ${txt_outfile}
76 && mv ${html_outfile.files_path}/meme.xml ${xml_outfile}
77 ]]>
78 </command>
79 <inputs>
80 <param format="fasta" name="input1" type="data" label="Sequences"/>
81 <conditional name="options_type">
82 <param name="options_type_selector" type="select" label="Options Configuration">
83 <option value="basic" selected="true">Basic</option>
84 <option value="advanced">Advanced</option>
85 </param>
86 <when value="basic" />
87 <when value="advanced">
88 <param name="sf" type="text" value="Galaxy FASTA Input" label="Name of sequence set" argument="-sf"/>
89 <conditional name="alphabet_type">
90 <param name="alphabet_type_selector" type="select" label="Sequence Alphabet">
91 <option value="protein">Protein</option>
92 <option value="dna" selected="true">DNA</option>
93 </param>
94 <when value="protein">
95 <conditional name="prior_type">
96 <param name="prior_type_selector" type="select" label="Choice of prior" argument="-prior">
97 <option value="dirichlet">simple Dirichlet prior</option>
98 <option value="dmix" selected="true">mixture of Dirichlets prior</option>
99 <option value="mega">extremely low variance dmix</option>
100 <option value="megap">mega for all but last iteration of EM; dmix on last iteration</option>
101 <option value="addone">add +1 to each observed count</option>
102 </param>
103 <when value="dirichlet">
104 <param name="prior_b" type="float" value="0.01" label="strength of prior on model parameters" argument="-b"/>
105 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
106 </when>
107 <when value="dmix">
108 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
109 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
110 </when>
111 <when value="mega">
112 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
113 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
114 </when>
115 <when value="megap">
116 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
117 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
118 </when>
119 <when value="addone" />
120 </conditional>
121 <conditional name="spmap_type">
122 <param name="spmap_type_selector" type="select" label="EM starting points" argument="-spmap">
123 <option value="uni">uni</option>
124 <option value="pam" selected="true">pam</option>
125 <option value="cons">Use starting point from string</option>
126 </param>
127 <when value="uni">
128 <param name="spfuzz" type="float" value="0.5" label="Fuzziness of the mapping" argument="-spfuzz"/>
129 </when>
130 <when value="pam">
131 <param name="spfuzz" type="integer" value="120" label="Fuzziness of the mapping" argument="-spfuzz"/>
132 </when>
133 <when value="cons">
134 <param name="cons" type="text" value="" label="Starting point from string" argument="-cons"/>
135 </when>
136 </conditional>
137 </when>
138 <when value="dna">
139 <param name="revcomp" label="Check reverse complement" type="boolean" truevalue="-revcomp" falsevalue="" checked="False"/>
140 <param name="pal" label="Check for palindromes" type="boolean" truevalue="-pal" falsevalue="" checked="False"/>
141 <conditional name="prior_type">
142 <param name="prior_type_selector" type="select" label="Sequence Alphabet" argument="-prior">
143 <option value="dirichlet" selected="true">simple Dirichlet prior</option>
144 <option value="dmix">mixture of Dirichlets prior</option>
145 <option value="mega">extremely low variance dmix</option>
146 <option value="megap">mega for all but last iteration of EM; dmix on last iteration</option>
147 <option value="addone">add +1 to each observed count</option>
148 </param>
149 <when value="dirichlet">
150 <param name="prior_b" type="float" value="0.01" label="strength of prior on model parameters" argument="-b"/>
151 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
152 </when>
153 <when value="dmix">
154 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
155 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
156 </when>
157 <when value="mega">
158 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
159 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
160 </when>
161 <when value="megap">
162 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
163 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
164 </when>
165 <when value="addone" />
166 </conditional>
167 <conditional name="spmap_type">
168 <param name="spmap_type_selector" type="select" label="EM starting points" argument="-spmap">
169 <option value="uni" selected="true">uni</option>
170 <option value="pam">pam</option>
171 <option value="cons">Use starting point from string</option>
172 </param>
173 <when value="uni">
174 <param name="spfuzz" type="float" value="0.5" label="Fuzziness of the mapping" argument="-spfuzz"/>
175 </when>
176 <when value="pam">
177 <param name="spfuzz" type="integer" value="120" label="Fuzziness of the mapping" argument="-spfuzz"/>
178 </when>
179 <when value="cons">
180 <param name="cons" type="text" value="" label="Starting point from string" argument="-cons"/>
181 </when>
182 </conditional>
183 </when>
184 </conditional>
185 <param name="nmotifs" type="integer" value="1" label="Number of different motifs to search" argument="-nmotifs" />
186 <param name="evt" type="float" value="inf" label="E-value to stop looking for motifs" argument="-evt"/>
187 <conditional name="mod_type">
188 <param name="mod_type_selector" type="select" label="Expected motif distribution" argument="-mod">
189 <option value="oops">One Occurrence Per Sequence</option>
190 <option value="zoops" selected="true">Zero or One Occurrence Per Sequence</option>
191 <option value="anr">Any Number of Repetitions</option>
192 </param>
193 <when value="oops" />
194 <when value="zoops">
195 <conditional name="motif_occurrence_type">
196 <param name="motif_occurrence_type_selector" type="select" label="Number of motif occurrences">
197 <option value="default" selected="true">Use defaults</option>
198 <option value="nsites">nsites</option>
199 <option value="min_max_sites">min and max sites</option>
200 </param>
201 <when value="default" />
202 <when value="nsites">
203 <param name="nsites" type="integer" value="1" label="Search nsites number of occurrences" argument="-nsites"/>
204 </when>
205 <when value="min_max_sites">
206 <param name="minsites" type="integer" value="1" label="minsites" argument="-minsites"/>
207 <param name="maxsites" type="integer" value="50" label="maxsites" argument="-maxsites"/>
208 </when>
209 </conditional>
210 </when>
211 <when value="anr">
212 <conditional name="motif_occurrence_type">
213 <param name="motif_occurrence_type_selector" type="select" label="Number of motif occurrences">
214 <option value="default" selected="true">Use defaults</option>
215 <option value="nsites">nsites</option>
216 <option value="min_max_sites">min and max sites</option>
217 </param>
218 <when value="default" />
219 <when value="nsites">
220 <param name="nsites" type="integer" value="1" label="Search nsites number of occurrences" argument="-nsites"/>
221 </when>
222 <when value="min_max_sites">
223 <param name="minsites" type="integer" value="1" label="minsites" argument="-minsites"/>
224 <param name="maxsites" type="integer" value="50" label="maxsites" argument="-maxsites"/>
225 </when>
226 </conditional>
227 </when>
228 </conditional>
229 <param name="wnsites" type="float" value="0.8" label="Weight on the prior on nsites" argument="-wnsites"/>
230 <conditional name="motif_width_type">
231 <param name="motif_width_type_selector" type="select" label="Motif width type">
232 <option value="exact">Exact width</option>
233 <option value="range" selected="true">Specify a range</option>
234 </param>
235 <when value="exact">
236 <param name="width" type="integer" value="10" label="Width of motif to search" argument="-w"/>
237 </when>
238 <when value="range">
239 <param name="minw" type="integer" value="8" label="Min width of motif to search" argument="-minw"/>
240 <param name="maxw" type="integer" value="50" label="Max width of motif to search" argument="-maxw"/>
241 </when>
242 </conditional>
243 <conditional name="motif_trim_type">
244 <param name="motif_trim_type_selector" type="select" label="Motif trim type">
245 <option value="nomatrim">No motif trim</option>
246 <option value="trim" selected="true">Trim motif</option>
247 </param>
248 <when value="nomatrim" />
249 <when value="trim">
250 <param name="wg" type="integer" value="11" label="Gap cost" argument="-wg"/>
251 <param name="ws" type="integer" value="1" label="Space cost" argument="-ws"/>
252 <param name="noendgaps" label="Do not penalize endgaps" type="boolean" truevalue="-noendgaps" falsevalue="" checked="False"/>
253 </when>
254 </conditional>
255 <param name="bfile" type="data" format="txt" optional="True" label="Background Model" argument="-bfile"/>
256 <param name="pspfile" type="data" format="txt" optional="True" label="Position-Specific Prior" argument="-psp"/>
257 <param name="maxiter" type="integer" value="50" label="Number of iterations of EM to run" argument="-maxiter"/>
258 <param name="distance" type="float" value="0.001" label="Convergence criterion" argument="-distance"/>
259 <conditional name="branching_type">
260 <param name="branching_type_selector" type="select" label="x-branching type">
261 <option value="x_branch">Perform x-branching</option>
262 <option value="no_x_branch" selected="true">No x-branching</option>
263 </param>
264 <when value="no_x_branch" />
265 <when value="x_branch">
266 <param name="bfactor" type="integer" value="3" label="Number of iterations of branching" argument="-bfactor"/>
267 <param name="heapsize" type="integer" value="64" label="Maximum number of heaps to use" argument="-heapsize"/>
268 </when>
269 </conditional>
270 </when>
271 </conditional>
272 <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">
273 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
274 </param>
275 </inputs>
276 <outputs>
277 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"/>
278 <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (text)"/>
279 <data format="memexml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)"/>
280 </outputs>
281 <tests>
282 <test>
283 <param name="input1" value="meme_input_1.fasta" ftype="fasta" dbkey="hg19"/>
284 <param name="options_type_selector" value="basic"/>
285 <param name="non_commercial_use" value="True"/>
286 <output name="html_outfile" file="meme_output_html_1.html" compare="contains"/>
287 <output name="txt_outfile" file="meme_output_txt_1.txt" lines_diff="12"/>
288 <output name="xml_outfile" file="meme_output_xml_1.xml" lines_diff="8"/>
289 </test>
290 <test>
291 <param name="input1" value="meme_input_1.fasta" ftype="fasta" dbkey="hg19"/>
292 <param name="options_type_selector" value="advanced"/>
293 <param name="plib" value="prior30.plib" ftype="txt"/>
294 <param name="non_commercial_use" value="True"/>
295 <output name="html_outfile" file="meme_output_html_2.html" compare="contains"/>
296 <output name="txt_outfile" file="meme_output_txt_2.txt" lines_diff="12"/>
297 <output name="xml_outfile" file="meme_output_xml_2.xml" lines_diff="8"/>
298 </test>
299 </tests>
300 <help>
301
302 .. class:: warningmark
303
304 **WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted.
305 Before using, be sure to review, agree, and comply with the license.**
306
307 If you want to specify sequence weights, you must include them at the top of your input FASTA file.
308
309 MEME discovers novel, ungapped motifs (recurring, fixed-length patterns) in your sequences (sample output from sequences).
310 MEME splits variable-length patterns into two or more separate motifs. A motif is a sequence pattern that occurs repeatedly
311 in a group of related sequences. MEME represents motifs as position-dependent letter-probability matrices which describe the
312 probability of each possible letter at each position in the pattern. Individual MEME motifs do not contain gaps. Patterns
313 with variable-length gaps are split by MEME into two or more separate motifs. MEME takes as input a group of sequences and
314 outputs as many motifs as requested. MEME uses statistical modeling techniques to automatically choose the best width, number
315 of occurrences, and description for each motif.
316
317 .. class:: infomark
318
319 For detailed information on MEME, click here_, or view the license_.
320
321 .. _here: http://meme-suite.org/doc/meme.html?man_type=web
322 .. _license: http://meme-suite.org/doc/copyright.html?man_type=web
323
324 </help>
325 <citations>
326 <citation type="bibtex">
327 @article{Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California,
328 author = {Bailey,Timothy L. and Elkan, Charles},
329 title = {Fitting a mixture model by expectation maximization to discover motifs in biopolymers},
330 year = {1994},
331 eprint = {None},
332 url = {http://www.sdsc.edu/~tbailey/papers/ismb94.pdf}
333 }</citation>
334 </citations>
335 </tool>