/tools/meme/meme.xml
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 <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 $options_type.evt < float('inf'): 17 -evt "${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>&1 || echo "Error running MEME." 78 79 80 && mv ${html_outfile.files_path}/meme.html ${html_outfile} 81 82 && mv ${html_outfile.files_path}/meme.txt ${txt_outfile} 83 84 && 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 333If 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:** 338Timothy 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 341For detailed information on MEME, click here_. To view the license_. 342 343------ 344 345**Citation** 346 347If 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>