/var/lib/mobyle/programs/consensus.xml is in mobyle-programs 5.1.2-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 | <?xml version='1.0' encoding='UTF-8'?>
<!-- XML Authors: Corinne Maufrais, Nicolas Joly and Bertrand Neron, -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>consensus</name>
<version>2004-04-14</version>
<doc>
<title>CONSENSUS</title>
<description>
<text lang="en">Identification of consensus patterns in unaligned DNA and protein sequences</text>
</description>
<authors>Gerald Z.Hertz, G.D. Stormo</authors>
<reference>G.Z. Hertz and G.D. Stormo. Identification of consensus patterns in unaligned DNA and protein sequences: a large-deviation statistical basis for penalizing gaps. In: Proceedings of the Third International Conference on Bioinformatics and Genome Research (H.A. Lim, and C.R. Cantor, editors). World Scientific Publishing Co., Ltd. Singapore, 1995. pages 201--216.</reference>
<homepagelink>http://gzhertz.home.comcast.net/~gzhertz/</homepagelink>
<sourcelink>http://gzhertz.home.comcast.net/~gzhertz/CONSENSUS_2004-04-14.TAR.gz</sourcelink>
</doc>
<category>sequence:protein:pattern</category>
<category>sequence:nucleic:pattern</category>
</head>
<parameters>
<parameter ismandatory="1" iscommand="1">
<name>prog</name>
<prompt lang="en">Program to run</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>consensus</value>
</vdef>
<vlist>
<velem>
<value>consensus</value>
<label>Search for fixed width patterns (consensus)</label>
</velem>
<velem>
<value>wconsensus</value>
<label>Same as consensus, width not fixed (wconsensus)</label>
</velem>
</vlist>
<format>
<code proglang="perl">"fasta-consensus <$sequence >$sequence.wcons ; $prog "</code>
<code proglang="python">"fasta-consensus <" + str(sequence) + " >" + str(sequence) + ".wcons ; " + str(prog)</code>
</format>
<argpos>0</argpos>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>sequence</name>
<prompt lang="en">Sequences file (-f)</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<format>
<code proglang="perl">" -f $sequence.wcons"</code>
<code proglang="python">" -f " + str(sequence) + ".wcons"</code>
</format>
<argpos>1</argpos>
</parameter>
<paragraph>
<name>required</name>
<prompt lang="en">Required parameter</prompt>
<argpos>2</argpos>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>width</name>
<prompt lang="en">Width of pattern for consensus program (-L)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$prog eq "consensus"</code>
<code proglang="python">prog == "consensus"</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -L$value" : ""</code>
<code proglang="python">( "" , " -L" + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>standard_deviation</name>
<prompt lang="en">Number of standard deviations to lower the information content at each position before identifying information peaks for wconsensus program (-s)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$prog eq "wconsensus"</code>
<code proglang="python">prog == "wconsensus"</code>
</precond>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">" -s$value"</code>
<code proglang="python">" -s" + str(value)</code>
</format>
<comment>
<text lang="en">A range of values should be tried. For example,
try values of 0.5, 1, 1.5, and 2. The overall best alignment is
the one having the smallest e-value.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>basic_options</name>
<prompt lang="en">Basic options</prompt>
<argpos>2</argpos>
<parameters>
<paragraph>
<name>alphabet_options</name>
<prompt lang="en">Alphabet options</prompt>
<parameters xmlns:xi="http://www.w3.org/2001/XInclude">
<parameter ismandatory="1" issimple="1">
<name>alphabet</name>
<prompt lang="en">Choose an alphabet</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>null</value>
</vdef>
<vlist>
<velem undef="1">
<value>null</value>
<label>Choose an alphabet</label>
</velem>
<velem>
<value>dna-alphabet</value>
<label>DNA</label>
</velem>
<velem>
<value>prot-alphabet</value>
<label>Protein</label>
</velem>
<velem>
<value>users</value>
<label>Users file</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value eq "dna-alphabet" or $value eq "prot-alphabet" )? "" : " -a <xi:include href="../../Local/Services/Programs/Env/consensus_data.xml" xpointer="xpointer(/alphabet/text())" />$value "</code>
<code proglang="python">("", " -a <xi:include href="../../Local/Services/Programs/Env/consensus_data.xml" xpointer="xpointer(/alphabet/text())" />"+ value)[ value in( "dna-alphabet" , "prot-alphabet" )]</code>
</format>
<ctrl>
<message>
<text lang="en">For 'User file' choice: A user alphabet file is mandatory</text>
</message>
<code proglang="perl">($value eq "users" and not defined $ascii_alphabet) or ($value eq "prot-alphabet" or $value eq "dna-alphabet" or $value eq "null")</code>
<code proglang="python">(value == "users" and ascii_alphabet is not None) or (value in ("prot-alphabet","dna-alphabet", "null") )</code>
</ctrl>
</parameter>
<parameter>
<name>ascii_alphabet</name>
<prompt lang="en">User Alphabet file (-a)</prompt>
<type>
<datatype>
<class>ConsensusAlphabet</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$alphabet eq "users"</code>
<code proglang="python">alphabet == "users"</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -a $value" : ""</code>
<code proglang="python">( "" , " -a " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">Each line contains a letter (a symbol in the alphabet) followed by an optional normalization number (default: 1.0). The normalization is based on the relative prior probabilities of the letters. For nucleic acids, this might be the genomic frequency of the bases; however, if the -d option is not used, the frequencies observed in your own sequence data are used. In nucleic acid alphabets, a letter and its complement appear on the same line, separated by a colon (a letter can be its own complement, e.g. when using a dimer alphabet).</text>
<text lang="en">Complementary letters may use the same normalization number. Only the standard 26 letters are permissible; however, when the -CS option is used, the alphabet is case sensitive so that a total of 52 different characters are possible.</text>
<text lang="en">POSSIBLE LINE FORMATS WITHOUT COMPLEMENTARY LETTERS:</text>
<text lang="en">letter</text>
<text lang="en">letter normalization</text>
<text lang="en">POSSIBLE LINE FORMATS WITH COMPLEMENTARY LETTERS:</text>
<text lang="en">letter:complement</text>
<text lang="en">letter:complement normalization</text>
<text lang="en">letter:complement normalization:complement's_normalization</text>
</comment>
</parameter>
<parameter>
<name>prior</name>
<prompt lang="en">Use the designated prior probabilities of the letters to override the observed frequencies (-d)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -d" : ""</code>
<code proglang="python">( "" , " -d" )[ value ]</code>
</format>
<comment>
<text lang="en">By default, the program uses the frequencies observed in your own sequence data for the prior probabilities of the letters. However, if the -d option is set, the prior probabilities designated by the alphabet options. If the -d option is not set, they are still used to determine the sequence alphabet, but any prior probability information is ignored.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<parameter>
<name>complement</name>
<prompt lang="en">Complement of nucleic acid sequences (-c)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<vlist>
<velem>
<value>0</value>
<label>Ignore the complementary strand (0)</label>
</velem>
<velem>
<value>1</value>
<label>Include both strands as separate sequences (1)</label>
</velem>
<velem>
<value>2</value>
<label>Include both strands as a single sequence (2)</label>
</velem>
<velem>
<value>3</value>
<label>Assume that the pattern is symmetrical (consensus program only) (3)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -c$value" : ""</code>
<code proglang="python">( "" , " -c" + str(value) )[ value is not None and value != vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Symmetrical pattern (3) is for the consensus program only</text>
</message>
<code proglang="perl">($value eq "3" and $prog eq "consensus") or ($value eq "0" or $value eq "1" or $value eq "2" )</code>
<code proglang="python">(value == "3" and prog == "consensus") or (value == "0" or value == "1" or value == "2" )</code>
</ctrl>
</parameter>
<parameter>
<name>max_cycle</name>
<prompt lang="en">How many words per matrix for each sequence to contribute</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>null</value>
</vdef>
<vlist>
<velem undef="1">
<value>null</value>
<label>No repeat</label>
</velem>
<velem>
<value>-n</value>
<label>Allow each sequence to contribute zero or more words per matrix (-n)</label>
</velem>
<velem>
<value>-N</value>
<label>Allow each sequence to contribute one or more words per matrix (-N)</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value ne $vdef) ? " $value$max_cycle_nb" : ""</code>
<code proglang="python">( "" , " " + str(value) + str(max_cycle_nb) )[ value != vdef ]</code>
</format>
<ctrl>
<message>
<text lang="en">For the -n/-N option, you must define a Maximum repeat of the matrix building cycle.</text>
</message>
<code proglang="perl">($value eq "-n" or $value eq "-N") and defined($max_cycle_nb)</code>
<code proglang="python">(value == "-n" or value =="-N") and max_cycle_nb is not None</code>
</ctrl>
<comment>
<text lang="en">-n integer: repeat the matrix building cycle a maximum of "integer"
times and allow each sequence to contribute zero or more words
per matrix.</text>
<text lang="en">-N integer: repeat the matrix building cycle a maximum of "integer"
times and allow each sequence to contribute one or more words
per matrix</text>
</comment>
</parameter>
<parameter>
<name>max_cycle_nb</name>
<prompt lang="en">Maximum repeat of the matrix building cycle for -n or -N</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>advenced_options</name>
<prompt lang="en">Advanced options</prompt>
<argpos>2</argpos>
<parameters>
<parameter>
<name>queue</name>
<prompt lang="en">Maximum number of matrices to save between cycles of the program (-q)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>200</value>
</vdef>
<format>
<code proglang="perl">(defined $value ) ? " -q $value" : ""</code>
<code proglang="python">( "" , " -q " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>distance</name>
<prompt lang="en">Minimum distance between the starting points of words within the same matrix pattern (-m)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$max_cycle ne "null"</code>
<code proglang="python">max_cycle != "null"</code>
</precond>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -m$value " : ""</code>
<code proglang="python">( "" , " -m" + str(value) )[ value is not None and value != vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">The value must be positive and this option can only be used when the "-n" or "-N" option is also used.</text>
</message>
<code proglang="perl">$value <= 0 and ($max_cycle == "-n" or $max_cycle == "-N")</code>
<code proglang="python">value > 0 and (max_cycle == "-n" or max_cycle == "-N")</code>
</ctrl>
<comment>
<text lang="en">The minimum distance between the starting points of words within the same matrix pattern; must be a positive integer; can only be used when the "-n" or "-N" option is also used.</text>
<text lang="en">For wconsensus, the default value is 1.</text>
<text lang="en">For consensus, this number is indicated by the width (-L).</text>
</comment>
</parameter>
<parameter>
<name>terminate</name>
<prompt lang="en">Terminate the program this number of cycles after the current most significant alignment is identified (-t)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -t$value " : ""</code>
<code proglang="python">( "" , " -t" + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">default: terminate only when the maximum number of matrix building cycles is completed.</text>
</comment>
</parameter>
<parameter>
<name>progeny</name>
<prompt lang="en">Save the top progeny matrices</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>-pr2</value>
</vdef>
<vlist>
<velem>
<value>-pr1</value>
<label>Regardless of parentage (-pr1)</label>
</velem>
<velem>
<value>-pr2</value>
<label>For each parental matrix (-pr2)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " $value" : ""</code>
<code proglang="python">( "" , " " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">-pr2 option prevents a strong pattern found in only a subset of the sequences from overwhelming the algorithm and eliminating other potential patterns. This undesirable situation can occur when a subset of the sequences share an evolutionary relationship not common to the majority of the sequences.</text>
</comment>
</parameter>
<parameter>
<name>linearly</name>
<prompt lang="en">Seed with the first sequence and proceed linearly through the list (-l)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -l" : ""</code>
<code proglang="python">( "" , " -l" )[ value ]</code>
</format>
<ctrl>
<message>
<text lang="en">The -l and -n option are mutually exclusive</text>
</message>
<code proglang="perl">($value == 1 and $max_cycle != "-n") or $value == 0</code>
<code proglang="python">(value == 1 and max_cycle != "-n") or value == 0</code>
</ctrl>
<comment>
<text lang="en">This option results in a significant speed up in the program, but the algorithm becomes dependent on the order of the sequence-file names.</text>
</comment>
</parameter>
<parameter>
<name>terminal_gap</name>
<prompt lang="en">Permit terminal gaps for wconsensus program</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">$prog eq "wconsensus"</code>
<code proglang="python">prog == "wconsensus"</code>
</precond>
<vdef>
<value>-pg0</value>
</vdef>
<vlist>
<velem>
<value>-pg0</value>
<label>Do NOT permit terminal gaps (-pg0)</label>
</velem>
<velem>
<value>-pg1</value>
<label>Permit penalized terminal gaps (-pg1)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " $value" : ""</code>
<code proglang="python">( "" , " " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>output_options</name>
<prompt lang="en">Output options</prompt>
<argpos>2</argpos>
<parameters>
<parameter>
<name>top_matrices</name>
<prompt lang="en">Number of top matrices to print (-pt)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>4</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -pt$value" : ""</code>
<code proglang="python">( "" , " -pt" + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">A negative value means print all the top matrices.</text>
</comment>
</parameter>
<parameter>
<name>final_matrices</name>
<prompt lang="en">Number of final matrices to print (-pf)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>4</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -pf$value" : ""</code>
<code proglang="python">( "" , " -pf" + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Default when NOT using -n or -N option: print 4 matrices; default when using -n or -N option: print no matrices.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>outfile</name>
<prompt>Results file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<format>
<code proglang="perl">" > $prog.results"</code>
<code proglang="python">" > " + str(prog) + ".results" </code>
</format>
<argpos>50</argpos>
<filenames>
<code proglang="perl">"$prog.results"</code>
<code proglang="python">str(prog) + ".results"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>consensus_format</name>
<prompt>wcons file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"*.wcons"</code>
<code proglang="python">"*.wcons"</code>
</filenames>
</parameter>
</parameters>
</program>
|