/var/lib/mobyle/programs/hmmbuild.xml is in mobyle-programs 5.1.2-2.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 | <?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>hmmbuild</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/hmmer_package.xml"/>
<doc>
<title>HMMBUILD</title>
<description>
<text lang="en">Build a profile HMM from an input multiple alignment</text>
</description>
</doc>
<category>hmm:building</category>
<command>hmmbuild</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>alignfile</name>
<prompt lang="en">Aligned sequences File</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>STOCKHOLM</dataFormat>
</type>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" "+str(value)</code>
</format>
<argpos>30</argpos>
</parameter>
<parameter issimple="1">
<name>alphabet</name>
<prompt lang="en">Forcing an alphabet in input alignment</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>null</value>
</vdef>
<vlist>
<velem undef="1">
<value>null</value>
<label>Autodetection</label>
</velem>
<velem>
<value>--amino</value>
<label>Protein</label>
</velem>
<velem>
<value>--dna</value>
<label>DNA</label>
</velem>
<velem>
<value>--rna</value>
<label>RNA</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">The alphabet type (amino, DNA, or RNA) is autodetected by default, by looking at the composition of the
msafile. Autodetection is normally quite reliable, but occasionally alphabet type may be ambiguous and
autodetection can fail (for instance, on tiny toy alignments of just a few residues). To avoid this, or to
increase robustness in automated analysis pipelines, you may specify the alphabet type of msafile with
these options.</text>
<text lang="en">Protein: Specify that all sequences in seqfile are proteins. By default, alphabet type is
autodetected from looking at the residue composition.</text>
<text lang="en">DNA: Specify that all sequences in seqfile are DNAs.</text>
<text lang="en">RNA: Specify that all sequences in seqfile are RNAs.</text>
</comment>
<argpos>2</argpos>
</parameter>
<parameter ishidden="1">
<name>hmm_textfile</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">" $alignfile.hmm"</code>
<code proglang="python">" " + str(alignfile) + ".hmm"</code>
</format>
<argpos>20</argpos>
</parameter>
<paragraph>
<name>output_options</name>
<prompt lang="en">Output options</prompt>
<argpos>1</argpos>
<parameters>
<parameter>
<name>hmmname</name>
<prompt lang="en">Name the HMM (-n)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -n $value" : ""</code>
<code proglang="python">( "" , " -n " + str(value) )[ value is not None ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Name the new profile. The default is to use the name of the alignment (if one
is present in the msafile, or, failing that, the name of the hmmfile. If msafile contains
more than one alignment, -n doesn't work, and every alignment must have a name
annotated in the msafile (as in Stockholm #=GF ID annotation).</text>
</comment>
</parameter>
<!--<parameter>
<name>save</name>
<prompt lang="en">Direct summary output to file, not stdout. (-o)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<format>
<code proglang="perl">($value)? " -o $value" : ""</code>
<code proglang="python">( "" , " -o " + str(value) )[ value is not None ]</code>
</format>
<argpos>1</argpos>
</parameter>
-->
<parameter>
<name>re_save</name>
<prompt lang="en">Re_save annotated, possibly modified MSA to 'file', in Stockholm format. (-O)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -O $value" : ""</code>
<code proglang="python">( "" , " -O " + str(value) )[ value is not None ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">After each model is constructed, resave annotated, possibly modified source alignments
to a file in Stockholm format. The alignments are annotated with a
reference annotation line indicating which columns were assigned as consensus,
and sequences are annotated with what relative sequence weights were assigned.
Some residues of the alignment may have been shifted to accommodate restrictions
of the Plan7 profile architecture, which disallows transitions between insert
and delete states..
</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>AlternativeConstruction</name>
<prompt lang="en">Alternative model construction strategies</prompt>
<argpos>1</argpos>
<comment>
<text lang="en">These options control how consensus columns are defined in an alignment.</text>
</comment>
<parameters>
<parameter>
<name>fast</name>
<prompt lang="en">Quickly and heuristically determine the architecture of the model (fast)
</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " --fast" : ""</code>
<code proglang="python">( "" , " --fast" )[ value ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Define consensus columns as those that have a fraction >= symfrac of residues
as opposed to gaps. (See the --symfrac option.) This is the default.</text>
</comment>
</parameter>
<parameter>
<name>symfrac</name>
<prompt lang="en">Sets sym fraction controlling for the --fast model construction algorithm, (symfrac) </prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$fast</code>
<code proglang="python">fast </code>
</precond>
<vdef>
<value>0.5</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " --symfrac $value" : ""</code>
<code proglang="python">( "" , " --symfrac " + str(value) )[ value is not None and value !=vdef ]
</code>
</format>
<comment>
<text lang="en">Enter a value >= 0 and <= 1. Define the residue fraction threshold necessary
to define a consensus column
when using the --fast option. The default is 0.5. The symbol fraction in each
column is calculated after taking relative sequence weighting into account, and ignoring
gap characters corresponding to ends of sequence fragments (as opposed
to internal insertions/deletions).
Setting this to 0.0 means that every alignment column will be assigned
as consensus, which may be useful in some cases. Setting it to 1.0
means that only columns that have no gap characters at all will be
assigned as consensus.
</text>
</comment>
<ctrl>
<message>
<text lang="en">Enter a value >= 0 and <= 1</text>
</message>
<code proglang="perl">0 <= $value <= 1 </code>
<code proglang="python">0 <= value <= 1 </code>
</ctrl>
</parameter>
<parameter>
<name>fragthresh</name>
<prompt lang="en">Tag sequence as a fragment, (fragthresh)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.5</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " --fragthresh $value" : ""</code>
<code proglang="python">( "" , " --fragthresh " + str(value) )[ value is not None and value !=vdef ] </code>
</format>
<comment>
<text lang="en">Enter a value >= 0 and <= 1. We only want to count terminal gaps as deletions if the aligned sequence is known
to be full-length, not if it is a fragment (for instance, because only part of it was
sequenced). HMMER uses a simple rule to infer fragments: if the sequence length
L is less than a fraction x times the mean sequence length of all the sequences
in the alignment, then the sequence is handled as a fragment. The default is 0.5.</text>
</comment>
<ctrl>
<message>
<text lang="en">Enter a value >= 0 and <= 1</text>
</message>
<code proglang="perl">0 <= $value <= 1 </code>
<code proglang="python">0 <= value <= 1 </code>
</ctrl>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>advanced</name>
<prompt lang="en">Advanced options</prompt>
<argpos>1</argpos>
<parameters>
<parameter>
<name>relativeWeight</name>
<prompt lang="en">Alternative relative sequence weighting strategies</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>wpb</value>
</vdef>
<vlist>
<velem>
<value>wpb</value>
<label>Henikoff position-based weighting scheme (wpb)</label>
</velem>
<velem>
<value>wgsc</value>
<label>Gerstein/Sonnhammer/Chothia ad hoc sequence weighting algorithm (wgsc)</label>
</velem>
<velem>
<value>wblosum</value>
<label>BLOSUM filtering algorithm to weight the sequences (wblosum)</label>
</velem>
<velem>
<value>wnone</value>
<label>Turn off all sequence weighting (wnone)</label>
</velem>
<velem>
<value>infoWgiven</value>
<label>Personal weights in file. Give file in next parameter</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value ne $vdef and $value ne 'infoWgiven') ? " --$value" : ""</code>
<code proglang="python">( "" , ' --'+ str(value) )[ value != vdef and value != 'infoWgiven' ]</code>
</format>
<comment>
<text lang="en">HMMER uses an ad hoc sequence weighting algorithm to downweight closely related sequences and upweight
distantly related ones. This has the effect of making models less biased by uneven phylogenetic
representation. For example, two identical sequences would typically each receive half the weight that one
sequence would. These options control which algorithm gets used.</text>
<text lang="en">wnp: Use the Henikoff position-based sequence weighting scheme [Henikoff and Henikoff,
J. Mol. Biol. 243:574, 1994]. This is the default.</text>
<text lang="en">wgsc: Use the Gerstein/Sonnhammer/Chothia weighting algorithm [Gerstein et al, J. Mol.
Biol. 235:1067, 1994].</text>
<text lang="en">wblosum: Use the same clustering scheme that was used to weight data in calculating BLOSUM
subsitution matrices [Henikoff and Henikoff, Proc. Natl. Acad. Sci 89:10915,
1992]. Sequences are single-linkage clustered at an identity threshold (default
0.62; see --wid) and within each cluster of c sequences, each sequence gets relative
weight 1/c.</text>
<text lang="en">wnone: No relative weights. All sequences are assigned uniform weight
</text>
</comment>
</parameter>
<parameter>
<name>wgiven</name>
<prompt lang="en">Personal weights in file </prompt>
<type>
<datatype>
<class>MSAFile</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$relativeWeight eq 'infoWgiven'</code>
<code proglang="python">relativeWeight == 'infoWgiven'</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " --wgiven $value" : "" </code>
<code proglang="python">("", "--wgiven " + str( value ))[value is not None] </code>
</format>
</parameter>
<parameter>
<name>wid</name>
<prompt lang="en">Set identity cutoff for BLOSUM filtering algorithm option (wid)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$wblosum eq 'wblosum' and not $eset</code>
<code proglang="python">relativeWeight == 'wblosum' and not eset</code>
</precond>
<vdef>
<value>0.62</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " --wid $value" : ""</code>
<code proglang="python">("", " --wid " + str(value))[value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Sets the identity threshold used by single-linkage clustering when using --wblosum.
Invalid with any other weighting scheme. Default is 0.62. Enter a value >= 0 and <= 1 </text>
</comment>
<ctrl>
<message>
<text lang="en">Enter a value >= 0 and <= 1</text>
</message>
<code proglang="perl">0 <= $value and $value <= 1 </code>
<code proglang="python">0 <= value and value <= 1 </code>
</ctrl>
</parameter>
<parameter>
<name>effectiveWeight</name>
<prompt lang="en">Alternate effective sequence weighting strategies</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $eset</code>
<code proglang="python">not eset</code>
</precond>
<vdef>
<value>--eent</value>
</vdef>
<vlist>
<velem>
<value>--eent</value>
<label>Adjust effective sequence weighting to achieve relative entropy target (eent)</label>
</velem>
<velem>
<value>--eclust</value>
<label>Effective sequence weighting is weighting of single linkage clusters (eclust)</label>
</velem>
<velem>
<value>--enone</value>
<label>No effective sequence weighting: just use number of sequence (enone)</label>
</velem>
<velem>
<value>turnOff</value>
<label>Personal setting of effective sequence weighting for all models to value</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value ne $vdef and $value ne 'turnOff') ? " $value" : ""</code>
<code proglang="python">( "" , " " +str(value) )[ value != vdef and value != 'turnOff']</code>
</format>
<comment>
<text lang="en">After relative weights are determined, they are normalized to sum to a total effective sequence number,
eff nseq. This number may be the actual number of sequences in the alignment, but it is almost always
smaller than that. The default entropy weighting method (--eent) reduces the effective sequence number
to reduce the information content (relative entropy, or average expected score on true homologs) per
consensus position. The target relative entropy is controlled by a two-parameter function, where the two
parameters are settable with --ere and --esigma.</text>
<text lang="en">--eent: Adjust effective sequence number to achieve a specific relative entropy per position
(see --ere). This is the default.</text>
<text lang="en">--eclust: Set effective sequence number to the number of single-linkage clusters at a specific
identity threshold (see --eid). This option is not recommended; it's for experiments
evaluating how much better --eent is.</text>
<text lang="en">--enone: Turn off effective sequence number determination and just use the actual number
of sequences. One reason you might want to do this is to try to maximize the
relative entropy/position of your model, which may be useful for short models</text>
</comment>
</parameter>
<parameter>
<name>eset</name>
<prompt lang="en">Set personal effective sequence weighting for all models to value (eset)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$effectiveWeight eq 'turnOff'</code>
<code proglang="python">effectiveWeight == 'turnOff'</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " --eset $value" : ""</code>
<code proglang="python">( "" , " --eset " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">Explicitly set the effective sequence number for all models to value</text>
</comment>
</parameter>
<parameter>
<name>ere</name>
<prompt lang="en">For personal adjustment of effective sequence weighting: set minimum relative entropy/position to value (ere)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$effectiveWeight eq "--eent"</code>
<code proglang="python">effectiveWeight == "--eent"</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " --ere $value" : ""</code>
<code proglang="python">( "" , " --ere " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">Set the minimum relative entropy/position target to value. Requires --eent. Default
depends on the sequence alphabet; for protein sequences, it is 0.59 bits/position.</text>
</comment>
</parameter>
<parameter>
<name>esigma</name>
<prompt lang="en">For personal adjustment of effective sequence weighting: set sigma parameter to value (esigma)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$effectiveWeight eq "--eent"</code>
<code proglang="python">effectiveWeight == "--eent"</code>
</precond>
<vdef>
<value>45.0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value!=$vdef) ? " --esigma $value" : ""</code>
<code proglang="python">( "" , " --esigma " + str(value) )[ value is not None and value !=vdef ]</code>
</format>
<comment>
<text lang="en">Sets the minimum relative entropy contributed by an entire model alignment, over
its whole length. This has the effect of making short models have higher relative
entropy per position than --ere alone would give. The default is 45.0 bits.</text>
</comment>
</parameter>
<parameter>
<name>eid</name>
<prompt lang="en">For single linkage clustering: set fractional identity cutoff to value (eid)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$effectiveWeight eq "--eclust" and not $eset</code>
<code proglang="python">effectiveWeight == "--eclust" and not eset</code>
</precond>
<vdef>
<value>0.62</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value!=$vdef) ? " --eid $value" : ""</code>
<code proglang="python">( "" , " --eid " + str(value) )[ value is not None and value !=vdef ]</code>
</format>
<comment>
<text lang="en">Enter a value >= 0 and <= 1. Sets the fractional pairwise identity cutoff used
by single linkage clustering with the --eclust option. The default is 0.62.</text>
</comment>
<ctrl>
<message>
<text lang="en">Enter a value >= 0 and <= 1</text>
</message>
<code proglang="perl">0 <= $value <= 1 </code>
<code proglang="python">0 <= value <= 1 </code>
</ctrl>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>ECalibration</name>
<prompt lang="en">Control of E-value calibration</prompt>
<argpos>1</argpos>
<comment>
<text lang="en">The location parameters for the expected score distributions for MSV filter scores,
Viterbi filter scores, and Forward scores require three short random sequence simulations.</text>
</comment>
<parameters>
<parameter>
<name>EmL</name>
<prompt lang="en">Lengt of sequences for MSV Gumbel mu fit (EmL)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>200</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value!=$vdef) ? " --EmL $value" : ""</code>
<code proglang="python">( "" , " --EmL " + str(value) )[ value is not None and value !=vdef ]</code>
</format>
<comment>
<text lang="en">Enter a value > 0. Sets the sequence length in simulation that estimates the location parameter mu
for MSV filter E-values. Default is 200.</text>
</comment>
<ctrl>
<message>
<text lang="en">Enter a value > 0 </text>
</message>
<code proglang="perl">$value > 0 </code>
<code proglang="python">value > 0 </code>
</ctrl>
</parameter>
<parameter>
<name>EmN</name>
<prompt lang="en">Number of sequences for MSV Gumbel mu fit (EmN)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>200</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value!=$vdef) ? " --EmN $value" : ""</code>
<code proglang="python">( "" , " --EmN " + str(value) )[ value is not None and value !=vdef ]</code>
</format>
<comment>
<text lang="en">Enter a value > 0. Sets the number of sequences in simulation that estimates the location parameter
mu for MSV filter E-values. Default is 200.</text>
</comment>
<ctrl>
<message>
<text lang="en">Enter a value > 0. </text>
</message>
<code proglang="perl">$value > 0 </code>
<code proglang="python">value > 0 </code>
</ctrl>
</parameter>
<parameter>
<name>EvL</name>
<prompt lang="en">Lengt of sequences for Viterbi Gumbel mu fit (EvL)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>200</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value!=$vdef) ? " --EvL $value" : ""</code>
<code proglang="python">( "" , " --EvL " + str(value) )[ value is not None and value !=vdef ]</code>
</format>
<comment>
<text lang="en">Enter a value > 0. Sets the sequence length in simulation that estimates the location parameter mu
for Viterbi filter E-values. Default is 200.</text>
</comment>
<ctrl>
<message>
<text lang="en">Enter a value > 0 </text>
</message>
<code proglang="perl">$value > 0 </code>
<code proglang="python">value > 0 </code>
</ctrl>
</parameter>
<parameter>
<name>EvN</name>
<prompt lang="en">Number of sequences for Viterbi Gumbel mu fit (EvN)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>200</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value!=$vdef) ? " --EvN $value" : ""</code>
<code proglang="python">( "" , " --EvN " + str(value) )[ value is not None and value !=vdef ]</code>
</format>
<comment>
<text lang="en">Enter a value > 0. Sets the number of sequences in simulation that estimates the location parameter
mu for Viterbi filter E-values. Default is 200.</text>
</comment>
<ctrl>
<message>
<text lang="en">Enter a value > 0.</text>
</message>
<code proglang="perl">$value > 0 </code>
<code proglang="python">value > 0 </code>
</ctrl>
</parameter>
<parameter>
<name>EfL</name>
<prompt lang="en">Lengt of sequences for Forward exp tail tau fit (EfL)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>100</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value!=$vdef) ? " --EfL $value" : ""</code>
<code proglang="python">( "" , " --EfL " + str(value) )[ value is not None and value !=vdef ]</code>
</format>
<comment>
<text lang="en">Enter a value > 0. Sets the sequence length in simulation that estimates the location parameter tau
for Forward E-values. Default is 100.</text>
</comment>
<ctrl>
<message>
<text lang="en">Enter a value > 0 </text>
</message>
<code proglang="perl">$value > 0 </code>
<code proglang="python">value > 0 </code>
</ctrl>
</parameter>
<parameter>
<name>EfN</name>
<prompt lang="en">Number of sequences for Forward exp tail tau fit (EfN)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>200</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value!=$vdef) ? " --EfN $value" : ""</code>
<code proglang="python">( "" , " --EfN " + str(value) )[ value is not None and value !=vdef ]</code>
</format>
<comment>
<text lang="en">Enter a value > 0. Sets the number of sequences in simulation that estimates the location parameter
tau for Forward E-values. Default is 200.</text>
</comment>
<ctrl>
<message>
<text lang="en">Enter a value > 0 </text>
</message>
<code proglang="perl">$value > 0 </code>
<code proglang="python">value > 0 </code>
</ctrl>
</parameter>
<parameter>
<name>Eft</name>
<prompt lang="en">Tail mass for Forward exponential tail tau fit (Eft)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.04</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value!=$vdef) ? " --Eft $value" : ""</code>
<code proglang="python">( "" , " --Eft " + str(value) )[ value is not None and value !=vdef ]</code>
</format>
<comment>
<text lang="en">Enter a value > 0 and < 1. Sets the tail mass fraction to fit in the simulation that estimates the location parameter
tau for Forward evalues. Default is 0.04.</text>
</comment>
<ctrl>
<message>
<text lang="en">Enter a value > 0 and < 1</text>
</message>
<code proglang="perl">$value > 0 and $value < 1</code>
<code proglang="python">value > 0 and value < 1</code>
</ctrl>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>other</name>
<prompt lang="en">Other options</prompt>
<argpos>1</argpos>
<parameters>
<parameter>
<name>seed</name>
<prompt lang="en">Set random number seed (seed)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>42</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " --seed $value" : ""</code>
<code proglang="python">( "" , " --seed " + str(value))[ value is not None and value != vdef ]</code>
</format>
<comment>
<text lang="en">Seed the random number generator with the value, an integer >= 0. If the value is nonzero,
any stochastic simulations will be reproducible; the same command will give the
same results. If the number is 0, the random number generator is seeded arbitrarily, and
stochastic simulations will vary from run to run of the same command. The default
seed is 42.</text>
</comment>
</parameter>
<parameter>
<name>laplace</name>
<prompt lang="en">Use a Laplace +1 prior</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " --laplace" : ""</code>
<code proglang="python">( "" , " --laplace " )[ value ]</code>
</format>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>hmmfile_res</name>
<prompt lang="en">Hmm profile</prompt>
<type>
<datatype>
<class>HmmProfile</class>
<superclass>AbstractText</superclass>
</datatype>
<dataFormat>HMMER3</dataFormat>
</type>
<filenames>
<code proglang="perl">*.hmm</code>
<code proglang="python">"*.hmm"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>re_save_file</name>
<prompt lang="en">Alignment file</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>STOCKHOLM</dataFormat>
</type>
<filenames>
<code proglang="perl">$re_save</code>
<code proglang="python">re_save</code>
</filenames>
</parameter>
</parameters>
</program>
|