/tools/meme/meme.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 353 lines · 300 code · 45 blank · 8 comment · 0 complexity · e85d93ff7b06ba543ed9b328f0ef307b MD5 · raw file 

    

  1. <tool id="meme_meme" name="MEME" version="1.0.0">
    2. 

  2.   <requirements><requirement type='package'>meme</requirement></requirements>
    3. 

  3.   <description>- Multiple Em for Motif Elicitation</description>
    4. 

  4.   <command>meme "$input1" -o "${html_outfile.files_path}" 
    5. 

  5.   -nostatus
    6. 

  6.   
    7. 

  7.   ##-p 8 ##number of processors
    8. 

  8.   
    9. 

  9.   #if str( $options_type.options_type_selector ) == 'advanced':
    10. 

  10.   -sf "${ str( $options_type.sf ).replace( ' ', '_' ) }"
    11. 

  11.   -${options_type.alphabet_type.alphabet_type_selector} 
    12. 

  12.   -mod "${options_type.mod_type.mod_type_selector}" 
    13. 

  13.   -nmotifs "${options_type.nmotifs}" 
    14. 

  14.   -wnsites "${options_type.wnsites}"
    15. 

  15.   
    16. 

  16.   #if $options_type.evt &lt; float('inf'):
    17. 

  17.     -evt "${options_type.evt}" 
    18. 

  18.   #end if
    19. 

  19.   
    20. 

  20.   #if str( $options_type.mod_type.mod_type_selector ) != 'oops':
    21. 

  21.     #if str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'nsites':
    22. 

  22.       -nsites "${options_type.mod_type.motif_occurrence_type.nsites}"
    23. 

  23.     #elif str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'min_max_sites':
    24. 

  24.       -minsites "${options_type.mod_type.motif_occurrence_type.minsites}" -maxsites "${options_type.mod_type.motif_occurrence_type.maxsites}"
    25. 

  25.     #end if
    26. 

  26.   #end if
    27. 

  27.   
    28. 

  28.   #if str( $options_type.motif_width_type.motif_width_type_selector ) == 'exact':
    29. 

  29.     -w "${options_type.motif_width_type.width}"
    30. 

  30.   #else
    31. 

  31.     -minw "${options_type.motif_width_type.minw}" -maxw "${options_type.motif_width_type.maxw}"
    32. 

  32.   #end if
    33. 

  33.   
    34. 

  34.   #if str( $options_type.motif_trim_type.motif_trim_type_selector ) == 'nomatrim':
    35. 

  35.     -nomatrim
    36. 

  36.   #else
    37. 

  37.     -wg "${options_type.motif_trim_type.wg}" -ws "${options_type.motif_trim_type.ws}" ${options_type.motif_trim_type.noendgaps}
    38. 

  38.   #end if
    39. 

  39.   
    40. 

  40.   #if str( $options_type.bfile ) != 'None':
    41. 

  41.     -bfile "${options_type.bfile}"
    42. 

  42.   #end if
    43. 

  43.   
    44. 

  44.   #if str( $options_type.pspfile ) != 'None':
    45. 

  45.     -psp "${options_type.pspfile}"
    46. 

  46.   #end if
    47. 

  47.   
    48. 

  48.   #if str( $options_type.alphabet_type.alphabet_type_selector ) == "dna":
    49. 

  49.     ${options_type.alphabet_type.revcomp} ${options_type.alphabet_type.pal}
    50. 

  50.   #end if
    51. 

  51.   
    52. 

  52.   -maxiter "${options_type.maxiter}" -distance "${options_type.distance}"
    53. 

  53.   
    54. 

  54.   -prior "${options_type.alphabet_type.prior_type.prior_type_selector}"
    55. 

  55.   #if str( $options_type.alphabet_type.prior_type.prior_type_selector ) != 'addone':
    56. 

  56.     -b "${options_type.alphabet_type.prior_type.prior_b}" 
    57. 

  57.     #if str( $options_type.alphabet_type.prior_type.plib ) != 'None':
    58. 

  58.       -plib "${options_type.alphabet_type.prior_type.plib}"
    59. 

  59.     #end if
    60. 

  60.   #end if
    61. 

  61.   
    62. 

  62.   #if str( $options_type.alphabet_type.spmap_type.spmap_type_selector ) == 'cons':
    63. 

  63.     -cons "${options_type.alphabet_type.spmap_type.cons}" 
    64. 

  64.   #else
    65. 

  65.     -spmap "${options_type.alphabet_type.spmap_type.spmap_type_selector}"
    66. 

  66.     -spfuzz "${options_type.alphabet_type.spmap_type.spfuzz}" 
    67. 

  67.   #end if
    68. 

  68.   
    69. 

  69.   #if str( $options_type.branching_type.branching_type_selector ) == 'x_branch':
    70. 

  70.     -x_branch -bfactor "${options_type.branching_type.bfactor}" -heapsize "${options_type.branching_type.heapsize}"
    71. 

  71.   #end if
    72. 

  72.   
    73. 

  73.   ##-maxsize "1000000" ##remove hardcoded maxsize? should increase number of processors instead
    74. 

  74.   
    75. 

  75.   #end if
    76. 

  76.   
    77. 

  77.   2&gt;&amp;1 || echo "Error running MEME."
    78. 

  78.   
    79. 

  79.   
    80. 

  80.   &amp;&amp; mv ${html_outfile.files_path}/meme.html ${html_outfile}
    81. 

  81.   
    82. 

  82.   &amp;&amp; mv ${html_outfile.files_path}/meme.txt ${txt_outfile}
    83. 

  83.   
    84. 

  84.   &amp;&amp; mv ${html_outfile.files_path}/meme.xml ${xml_outfile}
    85. 

  85.   
    86. 

  86.   </command>
    87. 

  87.   <inputs>
    88. 

  88.     <param format="fasta" name="input1" type="data" label="Sequences"/>
    89. 

  89.       
    90. 

  90.       <conditional name="options_type">
    91. 

  91.         <param name="options_type_selector" type="select" label="Options Configuration">
    92. 

  92.           <option value="basic" selected="true">Basic</option>
    93. 

  93.           <option value="advanced">Advanced</option>
    94. 

  94.         </param>
    95. 

  95.         <when value="basic">
    96. 

  96.           <!-- do nothing here -->
    97. 

  97.         </when>
    98. 

  98.         <when value="advanced">
    99. 

  99.       
    100. 

  100.       <param name="sf" type="text" value="Galaxy FASTA Input" label="Name of sequence set" />
    101. 

  101.       
    102. 

  102.       <conditional name="alphabet_type">
    103. 

  103.         <param name="alphabet_type_selector" type="select" label="Sequence Alphabet">
    104. 

  104.           <option value="protein">Protein</option>
    105. 

  105.           <option value="dna" selected="true">DNA</option>
    106. 

  106.         </param>
    107. 

  107.         <when value="protein">
    108. 

  108.           <conditional name="prior_type">
    109. 

  109.             <param name="prior_type_selector" type="select" label="Choice of prior">
    110. 

  110.               <option value="dirichlet">simple Dirichlet prior</option>
    111. 

  111.               <option value="dmix" selected="true">mixture of Dirichlets prior</option>
    112. 

  112.               <option value="mega">extremely low variance dmix</option>
    113. 

  113.               <option value="megap">mega for all but last iteration of EM; dmix on last iteration</option>
    114. 

  114.               <option value="addone">add +1 to each observed count</option>
    115. 

  115.             </param>
    116. 

  116.             <when value="dirichlet">
    117. 

  117.               <param name="prior_b" type="float" value="0.01" label="strength of prior on model parameters" />
    118. 

  118.               <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
    119. 

  119.             </when>
    120. 

  120.             <when value="dmix">
    121. 

  121.               <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" />
    122. 

  122.               <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
    123. 

  123.             </when>
    124. 

  124.             <when value="mega">
    125. 

  125.               <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" />
    126. 

  126.               <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
    127. 

  127.             </when>
    128. 

  128.             <when value="megap">
    129. 

  129.               <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" />
    130. 

  130.               <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
    131. 

  131.             </when>
    132. 

  132.             <when value="addone">
    133. 

  133.               <!-- no values here? -->
    134. 

  134.             </when>
    135. 

  135.           </conditional>
    136. 

  136.           <conditional name="spmap_type">
    137. 

  137.             <param name="spmap_type_selector" type="select" label="EM starting points">
    138. 

  138.               <option value="uni">uni</option>
    139. 

  139.               <option value="pam" selected="true">pam</option>
    140. 

  140.               <option value="cons">Use starting point from string</option>
    141. 

  141.             </param>
    142. 

  142.             <when value="uni">
    143. 

  143.               <param name="spfuzz" type="float" value="0.5" label="Fuzziness of the mapping" />
    144. 

  144.             </when>
    145. 

  145.             <when value="pam">
    146. 

  146.               <param name="spfuzz" type="integer" value="120" label="Fuzziness of the mapping" />
    147. 

  147.             </when>
    148. 

  148.             <when value="cons">
    149. 

  149.               <param name="cons" type="text" value="" label="Starting point from string" />
    150. 

  150.             </when>
    151. 

  151.           </conditional>
    152. 

  152.         </when>
    153. 

  153.         <when value="dna">
    154. 

  154.           <param name="revcomp" label="Check reverse complement" type="boolean" truevalue="-revcomp" falsevalue="" checked="False"/>
    155. 

  155.           <param name="pal" label="Check for palindromes" type="boolean" truevalue="-pal" falsevalue="" checked="False"/>
    156. 

  156.           <conditional name="prior_type">
    157. 

  157.             <param name="prior_type_selector" type="select" label="Sequence Alphabet">
    158. 

  158.               <option value="dirichlet" selected="true">simple Dirichlet prior</option>
    159. 

  159.               <option value="dmix">mixture of Dirichlets prior</option>
    160. 

  160.               <option value="mega">extremely low variance dmix</option>
    161. 

  161.               <option value="megap">mega for all but last iteration of EM; dmix on last iteration</option>
    162. 

  162.               <option value="addone">add +1 to each observed count</option>
    163. 

  163.             </param>
    164. 

  164.             <when value="dirichlet">
    165. 

  165.               <param name="prior_b" type="float" value="0.01" label="strength of prior on model parameters" />
    166. 

  166.               <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
    167. 

  167.             </when>
    168. 

  168.             <when value="dmix">
    169. 

  169.               <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" />
    170. 

  170.               <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
    171. 

  171.             </when>
    172. 

  172.             <when value="mega">
    173. 

  173.               <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" />
    174. 

  174.               <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
    175. 

  175.             </when>
    176. 

  176.             <when value="megap">
    177. 

  177.               <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" />
    178. 

  178.               <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
    179. 

  179.             </when>
    180. 

  180.             <when value="addone">
    181. 

  181.               <!-- no values here? -->
    182. 

  182.             </when>
    183. 

  183.           </conditional>
    184. 

  184.           <conditional name="spmap_type">
    185. 

  185.             <param name="spmap_type_selector" type="select" label="EM starting points">
    186. 

  186.               <option value="uni" selected="true">uni</option>
    187. 

  187.               <option value="pam">pam</option>
    188. 

  188.               <option value="cons">Use starting point from string</option>
    189. 

  189.             </param>
    190. 

  190.             <when value="uni">
    191. 

  191.               <param name="spfuzz" type="float" value="0.5" label="Fuzziness of the mapping" />
    192. 

  192.             </when>
    193. 

  193.             <when value="pam">
    194. 

  194.               <param name="spfuzz" type="integer" value="120" label="Fuzziness of the mapping" />
    195. 

  195.             </when>
    196. 

  196.             <when value="cons">
    197. 

  197.               <param name="cons" type="text" value="" label="Starting point from string" />
    198. 

  198.             </when>
    199. 

  199.           </conditional>
    200. 

  200.         </when>
    201. 

  201.       </conditional>
    202. 

  202.       
    203. 

  203.       <param name="nmotifs" type="integer" value="1" label="Number of different motifs to search" />
    204. 

  204.       <param name="evt" type="float" value="inf" label="E-value to stop looking for motifs" />
    205. 

  205.       <conditional name="mod_type">
    206. 

  206.         <param name="mod_type_selector" type="select" label="Expected motif distribution">
    207. 

  207.           <option value="oops">One Occurrence Per Sequence</option>
    208. 

  208.           <option value="zoops" selected="true">Zero or One Occurrence Per Sequence</option>
    209. 

  209.           <option value="anr">Any Number of Repetitions</option>
    210. 

  210.         </param>
    211. 

  211.         <when value="oops">
    212. 

  212.           <!-- no values here -->
    213. 

  213.         </when>
    214. 

  214.         <when value="zoops">
    215. 

  215.           <conditional name="motif_occurrence_type">
    216. 

  216.             <param name="motif_occurrence_type_selector" type="select" label="Number of motif occurrences">
    217. 

  217.               <option value="default" selected="true">Use defaults</option>
    218. 

  218.               <option value="nsites">nsites</option>
    219. 

  219.               <option value="min_max_sites">min and max sites</option>
    220. 

  220.             </param>
    221. 

  221.             <when value="default">
    222. 

  222.               <!-- no values here -->
    223. 

  223.             </when>
    224. 

  224.             <when value="nsites">
    225. 

  225.               <param name="nsites" type="integer" value="1" label="Search nsites number of occurrences" />
    226. 

  226.             </when>
    227. 

  227.             <when value="min_max_sites">
    228. 

  228.               <param name="minsites" type="integer" value="1" label="minsites" />
    229. 

  229.               <param name="maxsites" type="integer" value="50" label="maxsites" />
    230. 

  230.             </when>
    231. 

  231.           </conditional>
    232. 

  232.         </when>
    233. 

  233.         <when value="anr">
    234. 

  234.           <conditional name="motif_occurrence_type">
    235. 

  235.             <param name="motif_occurrence_type_selector" type="select" label="Number of motif occurrences">
    236. 

  236.               <option value="default" selected="true">Use defaults</option>
    237. 

  237.               <option value="nsites">nsites</option>
    238. 

  238.               <option value="min_max_sites">min and max sites</option>
    239. 

  239.             </param>
    240. 

  240.             <when value="default">
    241. 

  241.               <!-- no values here -->
    242. 

  242.             </when>
    243. 

  243.             <when value="nsites">
    244. 

  244.               <param name="nsites" type="integer" value="1" label="Search nsites number of occurrences" />
    245. 

  245.             </when>
    246. 

  246.             <when value="min_max_sites">
    247. 

  247.               <param name="minsites" type="integer" value="1" label="minsites" />
    248. 

  248.               <param name="maxsites" type="integer" value="50" label="maxsites" />
    249. 

  249.             </when>
    250. 

  250.           </conditional>
    251. 

  251.         </when>
    252. 

  252.       </conditional>
    253. 

  253.       <param name="wnsites" type="float" value="0.8" label="Weight on the prior on nsites" />
    254. 

  254.       
    255. 

  255.       <conditional name="motif_width_type">
    256. 

  256.         <param name="motif_width_type_selector" type="select" label="Motif width type">
    257. 

  257.           <option value="exact">Exact width</option>
    258. 

  258.           <option value="range" selected="true">Specify a range</option>
    259. 

  259.         </param>
    260. 

  260.         <when value="exact">
    261. 

  261.           <param name="width" type="integer" value="10" label="Width of motif to search" />
    262. 

  262.         </when>
    263. 

  263.         <when value="range">
    264. 

  264.           <param name="minw" type="integer" value="8" label="Min width of motif to search" />
    265. 

  265.           <param name="maxw" type="integer" value="50" label="Max width of motif to search" />
    266. 

  266.         </when>
    267. 

  267.       </conditional>
    268. 

  268.     
    269. 

  269.       <conditional name="motif_trim_type">
    270. 

  270.         <param name="motif_trim_type_selector" type="select" label="Motif trim type">
    271. 

  271.           <option value="nomatrim">No motif trim</option>
    272. 

  272.           <option value="trim" selected="true">Trim motif</option>
    273. 

  273.         </param>
    274. 

  274.         <when value="nomatrim">
    275. 

  275.           <!-- no values here -->
    276. 

  276.         </when>
    277. 

  277.         <when value="trim">
    278. 

  278.           <param name="wg" type="integer" value="11" label="Gap cost" />
    279. 

  279.           <param name="ws" type="integer" value="1" label="Space cost" />
    280. 

  280.           <param name="noendgaps" label="Do not penalize endgaps" type="boolean" truevalue="-noendgaps" falsevalue="" checked="False"/>
    281. 

  281.         </when>
    282. 

  282.       </conditional>
    283. 

  283.     
    284. 

  284.     <param name="bfile" type="data" format="txt" optional="True" label="Background Model" />
    285. 

  285.     <param name="pspfile" type="data" format="txt" optional="True" label="Position-Specific Prior" />
    286. 

  286.     
    287. 

  287.     <param name="maxiter" type="integer" value="50" label="Number of iterations of EM to run" />
    288. 

  288.     <param name="distance" type="float" value="0.001" label="Convergence criterion" />
    289. 

  289.     
    290. 

  290.       <conditional name="branching_type">
    291. 

  291.         <param name="branching_type_selector" type="select" label="x-branching type">
    292. 

  292.           <option value="x_branch">Perform x-branching</option>
    293. 

  293.           <option value="no_x_branch" selected="true">No x-branching</option>
    294. 

  294.         </param>
    295. 

  295.         <when value="no_x_branch">
    296. 

  296.           <!-- no values here -->
    297. 

  297.         </when>
    298. 

  298.         <when value="x_branch">
    299. 

  299.           <param name="bfactor" type="integer" value="3" label="Number of iterations of branching" />
    300. 

  300.           <param name="heapsize" type="integer" value="64" label="Maximum number of heaps to use" />
    301. 

  301.         </when>
    302. 

  302.       </conditional>
    303. 

  303.   
    304. 

  304.     </when>
    305. 

  305.   </conditional>
    306. 

  306.   
    307. 

  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. 

  308.     <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
    309. 

  309.   </param>
    310. 

  310.   
    311. 

  311.   </inputs>
    312. 

  312.   <outputs>
    313. 

  313.     <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"/>
    314. 

  314.     <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (text)"/>
    315. 

  315.     <data format="memexml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)"/>
    316. 

  316.   </outputs>
    317. 

  317.   <tests>
    318. 

  318.     <test>
    319. 

  319.       <param name="input1" value="meme/meme/meme_input_1.fasta" ftype="fasta" dbkey="hg19"/>
    320. 

  320.       <param name="options_type_selector" value="basic"/>
    321. 

  321.       <param name="non_commercial_use" value="True"/>
    322. 

  322.       <output name="html_outfile" file="meme/meme/meme_output_html_1.html" lines_diff="12"/>
    323. 

  323.       <output name="txt_outfile" file="meme/meme/meme_output_txt_1.txt" lines_diff="12"/>
    324. 

  324.       <output name="xml_outfile" file="meme/meme/meme_output_xml_1.xml" lines_diff="8"/>
    325. 

  325.     </test>
    326. 

  326.   </tests>
    327. 

  327.   <help>
    328. 

  328. 

  329. .. class:: warningmark
    330. 

  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. 

  332. 

  333. If you want to specify sequence weights, you must include them at the top of your input FASTA file.
    334. 

  334. 

  335. .. class:: infomark
    336. 

  336. 

  337. **To cite MEME:**
    338. 

  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. 

  339. 

  340. 

  341. For detailed information on MEME, click here_. To view the license_.
    342. 

  342. 

  343. ------
    344. 

  344. 

  345. **Citation**
    346. 

  346. 

  347. If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
    348. 

  348. 

  349. .. _here: http://meme.nbcr.net/meme/meme-intro.html
    350. 

  350. .. _license: http://meme.nbcr.net/meme/COPYRIGHT.html
    351. 

  351. 

  352.   </help>
    353. 

  353. </tool>
    354.