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comparison meme.xml @ 0:16752a2d49c4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
author iuc
date Mon, 21 Dec 2015 05:45:38 -0500
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children 90e9d7f994c4
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1 <tool id="meme_meme" name="MEME" version="4.11.0.0">
2 <description>- Multiple Em for Motif Elicitation</description>
3 <requirements>
4 <requirement type="package" version="4.11.0">meme</requirement>
5 </requirements>
6 <command>
7 <![CDATA[
8 meme "$input1"
9 -o "${html_outfile.files_path}"
10 -nostatus
11 #if str( $options_type.options_type_selector ) == 'advanced':
12 -sf "${ str( $options_type.sf ).replace( ' ', '_' ) }"
13 -${options_type.alphabet_type.alphabet_type_selector}
14 -mod "${options_type.mod_type.mod_type_selector}"
15 -nmotifs "${options_type.nmotifs}"
16 -wnsites "${options_type.wnsites}"
17 #if $options_type.evt < float('inf'):
18 -evt "${options_type.evt}"
19 #end if
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}"
25 -maxsites "${options_type.mod_type.motif_occurrence_type.maxsites}"
26 #end if
27 #end if
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 "${options_type.motif_width_type.minw}"
32 -maxw "${options_type.motif_width_type.maxw}"
33 #end if
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}"
38 -ws "${options_type.motif_trim_type.ws}"
39 ${options_type.motif_trim_type.noendgaps}
40 #end if
41 #if str( $options_type.bfile ) != 'None':
42 -bfile "${options_type.bfile}"
43 #end if
44 #if str( $options_type.pspfile ) != 'None':
45 -psp "${options_type.pspfile}"
46 #end if
47 #if str( $options_type.alphabet_type.alphabet_type_selector ) == "dna":
48 ${options_type.alphabet_type.revcomp} ${options_type.alphabet_type.pal}
49 #end if
50 -maxiter "${options_type.maxiter}"
51 -distance "${options_type.distance}"
52 -prior "${options_type.alphabet_type.prior_type.prior_type_selector}"
53 #if str( $options_type.alphabet_type.prior_type.prior_type_selector ) != 'addone':
54 -b "${options_type.alphabet_type.prior_type.prior_b}"
55 #if str( $options_type.alphabet_type.prior_type.plib ) != 'None':
56 -plib "${options_type.alphabet_type.prior_type.plib}"
57 #end if
58 #end if
59 #if str( $options_type.alphabet_type.spmap_type.spmap_type_selector ) == 'cons':
60 -cons "${options_type.alphabet_type.spmap_type.cons}"
61 #else
62 -spmap "${options_type.alphabet_type.spmap_type.spmap_type_selector}"
63 -spfuzz "${options_type.alphabet_type.spmap_type.spfuzz}"
64 #end if
65 #if str( $options_type.branching_type.branching_type_selector ) == 'x_branch':
66 -x_branch
67 -bfactor "${options_type.branching_type.bfactor}"
68 -heapsize "${options_type.branching_type.heapsize}"
69 #end if
70 #end if
71 2>&1 || echo "Error running MEME."
72 && mv ${html_outfile.files_path}/meme.html ${html_outfile}
73 && mv ${html_outfile.files_path}/meme.txt ${txt_outfile}
74 && mv ${html_outfile.files_path}/meme.xml ${xml_outfile}
75 ]]>
76 </command>
77 <inputs>
78 <param format="fasta" name="input1" type="data" label="Sequences"/>
79 <conditional name="options_type">
80 <param name="options_type_selector" type="select" label="Options Configuration">
81 <option value="basic" selected="true">Basic</option>
82 <option value="advanced">Advanced</option>
83 </param>
84 <when value="basic" />
85 <when value="advanced">
86 <param name="sf" type="text" value="Galaxy FASTA Input" label="Name of sequence set" argument="-sf"/>
87 <conditional name="alphabet_type">
88 <param name="alphabet_type_selector" type="select" label="Sequence Alphabet">
89 <option value="protein">Protein</option>
90 <option value="dna" selected="true">DNA</option>
91 </param>
92 <when value="protein">
93 <conditional name="prior_type">
94 <param name="prior_type_selector" type="select" label="Choice of prior" argument="-prior">
95 <option value="dirichlet">simple Dirichlet prior</option>
96 <option value="dmix" selected="true">mixture of Dirichlets prior</option>
97 <option value="mega">extremely low variance dmix</option>
98 <option value="megap">mega for all but last iteration of EM; dmix on last iteration</option>
99 <option value="addone">add +1 to each observed count</option>
100 </param>
101 <when value="dirichlet">
102 <param name="prior_b" type="float" value="0.01" label="strength of prior on model parameters" argument="-b"/>
103 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
104 </when>
105 <when value="dmix">
106 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
107 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
108 </when>
109 <when value="mega">
110 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
111 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
112 </when>
113 <when value="megap">
114 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
115 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
116 </when>
117 <when value="addone" />
118 </conditional>
119 <conditional name="spmap_type">
120 <param name="spmap_type_selector" type="select" label="EM starting points" argument="-spmap">
121 <option value="uni">uni</option>
122 <option value="pam" selected="true">pam</option>
123 <option value="cons">Use starting point from string</option>
124 </param>
125 <when value="uni">
126 <param name="spfuzz" type="float" value="0.5" label="Fuzziness of the mapping" argument="-spfuzz"/>
127 </when>
128 <when value="pam">
129 <param name="spfuzz" type="integer" value="120" label="Fuzziness of the mapping" argument="-spfuzz"/>
130 </when>
131 <when value="cons">
132 <param name="cons" type="text" value="" label="Starting point from string" argument="-cons"/>
133 </when>
134 </conditional>
135 </when>
136 <when value="dna">
137 <param name="revcomp" label="Check reverse complement" type="boolean" truevalue="-revcomp" falsevalue="" checked="False"/>
138 <param name="pal" label="Check for palindromes" type="boolean" truevalue="-pal" falsevalue="" checked="False"/>
139 <conditional name="prior_type">
140 <param name="prior_type_selector" type="select" label="Sequence Alphabet" argument="-prior">
141 <option value="dirichlet" selected="true">simple Dirichlet prior</option>
142 <option value="dmix">mixture of Dirichlets prior</option>
143 <option value="mega">extremely low variance dmix</option>
144 <option value="megap">mega for all but last iteration of EM; dmix on last iteration</option>
145 <option value="addone">add +1 to each observed count</option>
146 </param>
147 <when value="dirichlet">
148 <param name="prior_b" type="float" value="0.01" label="strength of prior on model parameters" argument="-b"/>
149 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
150 </when>
151 <when value="dmix">
152 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
153 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
154 </when>
155 <when value="mega">
156 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
157 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
158 </when>
159 <when value="megap">
160 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
161 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
162 </when>
163 <when value="addone" />
164 </conditional>
165 <conditional name="spmap_type">
166 <param name="spmap_type_selector" type="select" label="EM starting points" argument="-spmap">
167 <option value="uni" selected="true">uni</option>
168 <option value="pam">pam</option>
169 <option value="cons">Use starting point from string</option>
170 </param>
171 <when value="uni">
172 <param name="spfuzz" type="float" value="0.5" label="Fuzziness of the mapping" argument="-spfuzz"/>
173 </when>
174 <when value="pam">
175 <param name="spfuzz" type="integer" value="120" label="Fuzziness of the mapping" argument="-spfuzz"/>
176 </when>
177 <when value="cons">
178 <param name="cons" type="text" value="" label="Starting point from string" argument="-cons"/>
179 </when>
180 </conditional>
181 </when>
182 </conditional>
183 <param name="nmotifs" type="integer" value="1" label="Number of different motifs to search" argument="-nmotifs" />
184 <param name="evt" type="float" value="inf" label="E-value to stop looking for motifs" argument="-evt"/>
185 <conditional name="mod_type">
186 <param name="mod_type_selector" type="select" label="Expected motif distribution" argument="-mod">
187 <option value="oops">One Occurrence Per Sequence</option>
188 <option value="zoops" selected="true">Zero or One Occurrence Per Sequence</option>
189 <option value="anr">Any Number of Repetitions</option>
190 </param>
191 <when value="oops" />
192 <when value="zoops">
193 <conditional name="motif_occurrence_type">
194 <param name="motif_occurrence_type_selector" type="select" label="Number of motif occurrences">
195 <option value="default" selected="true">Use defaults</option>
196 <option value="nsites">nsites</option>
197 <option value="min_max_sites">min and max sites</option>
198 </param>
199 <when value="default" />
200 <when value="nsites">
201 <param name="nsites" type="integer" value="1" label="Search nsites number of occurrences" argument="-nsites"/>
202 </when>
203 <when value="min_max_sites">
204 <param name="minsites" type="integer" value="1" label="minsites" argument="-minsites"/>
205 <param name="maxsites" type="integer" value="50" label="maxsites" argument="-maxsites"/>
206 </when>
207 </conditional>
208 </when>
209 <when value="anr">
210 <conditional name="motif_occurrence_type">
211 <param name="motif_occurrence_type_selector" type="select" label="Number of motif occurrences">
212 <option value="default" selected="true">Use defaults</option>
213 <option value="nsites">nsites</option>
214 <option value="min_max_sites">min and max sites</option>
215 </param>
216 <when value="default" />
217 <when value="nsites">
218 <param name="nsites" type="integer" value="1" label="Search nsites number of occurrences" argument="-nsites"/>
219 </when>
220 <when value="min_max_sites">
221 <param name="minsites" type="integer" value="1" label="minsites" argument="-minsites"/>
222 <param name="maxsites" type="integer" value="50" label="maxsites" argument="-maxsites"/>
223 </when>
224 </conditional>
225 </when>
226 </conditional>
227 <param name="wnsites" type="float" value="0.8" label="Weight on the prior on nsites" argument="-wnsites"/>
228 <conditional name="motif_width_type">
229 <param name="motif_width_type_selector" type="select" label="Motif width type">
230 <option value="exact">Exact width</option>
231 <option value="range" selected="true">Specify a range</option>
232 </param>
233 <when value="exact">
234 <param name="width" type="integer" value="10" label="Width of motif to search" argument="-w"/>
235 </when>
236 <when value="range">
237 <param name="minw" type="integer" value="8" label="Min width of motif to search" argument="-minw"/>
238 <param name="maxw" type="integer" value="50" label="Max width of motif to search" argument="-maxw"/>
239 </when>
240 </conditional>
241 <conditional name="motif_trim_type">
242 <param name="motif_trim_type_selector" type="select" label="Motif trim type">
243 <option value="nomatrim">No motif trim</option>
244 <option value="trim" selected="true">Trim motif</option>
245 </param>
246 <when value="nomatrim" />
247 <when value="trim">
248 <param name="wg" type="integer" value="11" label="Gap cost" argument="-wg"/>
249 <param name="ws" type="integer" value="1" label="Space cost" argument="-ws"/>
250 <param name="noendgaps" label="Do not penalize endgaps" type="boolean" truevalue="-noendgaps" falsevalue="" checked="False"/>
251 </when>
252 </conditional>
253 <param name="bfile" type="data" format="txt" optional="True" label="Background Model" argument="-bfile"/>
254 <param name="pspfile" type="data" format="txt" optional="True" label="Position-Specific Prior" argument="-psp"/>
255 <param name="maxiter" type="integer" value="50" label="Number of iterations of EM to run" argument="-maxiter"/>
256 <param name="distance" type="float" value="0.001" label="Convergence criterion" argument="-distance"/>
257 <conditional name="branching_type">
258 <param name="branching_type_selector" type="select" label="x-branching type">
259 <option value="x_branch">Perform x-branching</option>
260 <option value="no_x_branch" selected="true">No x-branching</option>
261 </param>
262 <when value="no_x_branch" />
263 <when value="x_branch">
264 <param name="bfactor" type="integer" value="3" label="Number of iterations of branching" argument="-bfactor"/>
265 <param name="heapsize" type="integer" value="64" label="Maximum number of heaps to use" argument="-heapsize"/>
266 </when>
267 </conditional>
268 </when>
269 </conditional>
270 <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">
271 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
272 </param>
273 </inputs>
274 <outputs>
275 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"/>
276 <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (text)"/>
277 <data format="memexml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)"/>
278 </outputs>
279 <tests>
280 <test>
281 <param name="input1" value="meme_input_1.fasta" ftype="fasta" dbkey="hg19"/>
282 <param name="options_type_selector" value="basic"/>
283 <param name="non_commercial_use" value="True"/>
284 <output name="html_outfile" file="meme_output_html_1.html" compare="contains"/>
285 <output name="txt_outfile" file="meme_output_txt_1.txt" lines_diff="12"/>
286 <output name="xml_outfile" file="meme_output_xml_1.xml" lines_diff="8"/>
287 </test>
288 <test>
289 <param name="input1" value="meme_input_1.fasta" ftype="fasta" dbkey="hg19"/>
290 <param name="options_type_selector" value="advanced"/>
291 <param name="plib" value="prior30.plib" ftype="txt"/>
292 <param name="non_commercial_use" value="True"/>
293 <output name="html_outfile" file="meme_output_html_2.html" compare="contains"/>
294 <output name="txt_outfile" file="meme_output_txt_2.txt" lines_diff="12"/>
295 <output name="xml_outfile" file="meme_output_xml_2.xml" lines_diff="8"/>
296 </test>
297 </tests>
298 <help>
299
300 .. class:: warningmark
301
302 **WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted.
303 Before using, be sure to review, agree, and comply with the license.**
304
305 If you want to specify sequence weights, you must include them at the top of your input FASTA file.
306
307 MEME discovers novel, ungapped motifs (recurring, fixed-length patterns) in your sequences (sample output from sequences).
308 MEME splits variable-length patterns into two or more separate motifs. A motif is a sequence pattern that occurs repeatedly
309 in a group of related sequences. MEME represents motifs as position-dependent letter-probability matrices which describe the
310 probability of each possible letter at each position in the pattern. Individual MEME motifs do not contain gaps. Patterns
311 with variable-length gaps are split by MEME into two or more separate motifs. MEME takes as input a group of sequences and
312 outputs as many motifs as requested. MEME uses statistical modeling techniques to automatically choose the best width, number
313 of occurrences, and description for each motif.
314
315 .. class:: infomark
316
317 For detailed information on MEME, click here_, or view the license_.
318
319 .. _here: http://meme-suite.org/doc/meme.html?man_type=web
320 .. _license: http://meme-suite.org/doc/copyright.html?man_type=web
321
322 </help>
323 <citations>
324 <citation type="bibtex">
325 @published{Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California,
326 author = {Bailey,Timothy L. and Elkan, Charles},
327 title = {Fitting a mixture model by expectation maximization to discover motifs in biopolymers},
328 year = {1994},
329 eprint = {None},
330 url = {http://www.sdsc.edu/~tbailey/papers/ismb94.pdf}
331 }</citation>
332 </citations>
333 </tool>