/var/lib/mobyle/programs/hmmsearch.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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 | <?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>hmmsearch</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/hmmer_package.xml"/>
<doc>
<title>HMMSEARCH</title>
<description>
<text lang="en">Search a sequence database with a profile HMM</text>
</description>
<comment>
<text lang="en">hmmsearch reads an HMM from hmmfile and searches seqfile for significantly similar sequence matches.</text>
<text lang="en">hmmsearch may take minutes or even hours to run, depending on the size of the sequence database.</text>
<text lang="en">The output consists of four sections: a ranked list of the best scoring sequences, a ranked list of the best scoring domains, alignments for all the best scoring domains, and a histogram of the scores. sequence score may be higher than a domain score for the same sequence if there is more than domain in the sequence; the sequence score takes into account all the domains. All sequences scoring above the -E and -T cutoffs are shown in the first list, then every domain found in this list is shown in the second list of domain hits. If desired, E-value and bit score thresholds may also be applied to the domain list using the --domE and --domT options.</text>
</comment>
</doc>
<category>hmm:database:search</category>
<category>database:search:hmm</category>
<command>hmmsearch</command>
</head>
<parameters xmlns:xi="http://www.w3.org/2001/XInclude">
<parameter ismandatory="1" issimple="1">
<name>hmmfile</name>
<prompt lang="en">HMM file</prompt>
<type>
<datatype>
<class>HmmProfile</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" "+str(value)</code>
</format>
<argpos>2</argpos>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>public_seq_DB</name>
<prompt lang="en">Choose one public protein sequence database</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $public_seq_DB </code>
<code proglang="python">not perso_seq_DB or ( perso_seq_DB and public_seq_DB )</code>
</precond>
<vdef>
<value>null</value>
</vdef>
<xi:include href="../../Local/Services/Programs/Env/protdbs.xml">
<xi:fallback>
<vlist>
<velem undef="1">
<value>null</value>
<label>Choose a database</label>
</velem>
</vlist>
</xi:fallback>
</xi:include>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" "+str(value)</code>
</format>
<ctrl>
<message>
<text lang="en">Can not handle both public AND personal protein sequence database at the same time </text>
</message>
<code proglang="perl">not defined $perso_seq_DB</code>
<code proglang="python">not perso_seq_DB</code>
</ctrl>
<argpos>3</argpos>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>perso_seq_DB</name>
<prompt lang="en">OR paste a personal protein sequence database</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<precond>
<code proglang="perl">not $perso_seq_DB </code>
<code proglang="python">not public_seq_DB or ( perso_seq_DB and public_seq_DB )</code>
</precond>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" "+str(value)</code>
</format>
<ctrl>
<message>
<text lang="en">Can not handle both public AND personal protein sequence database at the same time </text>
</message>
<code proglang="perl">not defined $perso_seq_DB</code>
<code proglang="python">not public_seq_DB</code>
</ctrl>
<argpos>3</argpos>
</parameter>
<paragraph>
<name>thresholds_report</name>
<prompt lang="en">Options controlling reporting thresholds</prompt>
<argpos>1</argpos>
<comment>
<text lang="en">'Reporting' thresholds control which hits are reported in output files. Sequence hits and
domain hits are ranked by statistical significance (E-value) and output is
generated in two sections called 'per-target' and 'per-domain' output. In per-target output, by default, all
sequence hits with an E-value <= 10 are reported. In the per-domain output, for each target that has passed
per-target reporting thresholds, all domains satisfying per-domain reporting thresholds are reported. By default,
these are domains with conditional E-values of <= 10. The following options allow you to change the
default E-value reporting thresholds, or to use bit score thresholds instead.</text>
</comment>
<parameters>
<parameter issimple="1">
<name>E_value_cutoff</name>
<prompt lang="en">E_value cutoff (-E)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">not defined $Bit_cutoff and $model_specific ne '--cut_ga' and $model_specific ne '--cut_nc'</code>
<code proglang="python">Bit_cutoff is None and model_specific != '--cut_ga' and model_specific != '--cut_nc'</code>
</precond>
<vdef>
<value>10.0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -E $value" : ""</code>
<code proglang="python">( "" , " -E " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">In the per-target output, report target profiles with an E-value of <= value. The
default is 10.0, meaning that on average, about 10 false positives will be reported
per query, so you can see the top of the 'noise' and decide for yourself if it's really
noise.</text>
</comment>
</parameter>
<parameter>
<name>Bit_cutoff</name>
<prompt lang="en">Bit score cutoff (-T)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$E_value_cutoff == 10.0 and $model_specific ne '--cut_ga' and $model_specific ne '--cut_nc'</code>
<code proglang="python">E_value_cutoff == 10.0 and model_specific != '--cut_ga' and model_specific != '--cut_nc'</code>
</precond>
<format>
<code proglang="perl">(defined $value)? " -T $value" : ""</code>
<code proglang="python">( "" , " -T " + str(value) )[ value is not None ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Instead of thresholding per-profile output on E-value, instead report target profiles
with a bit score of >= value.</text>
</comment>
</parameter>
<parameter>
<name>domE</name>
<prompt lang="en">E-value cutoff for the per-domain ranked hit list (--domE)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">not defined $domT and $model_specific ne '--cut_ga' and $model_specific ne '--cut_nc'</code>
<code proglang="python">domT is None and model_specific != '--cut_ga' and model_specific != '--cut_nc'</code>
</precond>
<vdef>
<value>10.0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " --domE $value" : ""</code>
<code proglang="python">( "" , " --domE " + str(value) )[ value is not None and value !=vdef ]</code>
</format>
<comment>
<text lang="en">In the per-domain output, for target profiles that have already satisfied the perprofile
reporting threshold, report individual domains with a conditional E-value
of <= value. The default is 10.0. A 'conditional' E-value means the expected
number of additional false positive domains in the smaller search space of those
comparisons that already satisfied the per-profile reporting threshold (and thus
must have at least one homologous domain already).</text>
</comment>
</parameter>
<parameter>
<name>domT</name>
<prompt lang="en">Bit score cutoff for the per-domain ranked hit list (--domT)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$domE == 10.0 and $model_specific ne '--cut_ga' and $model_specific ne '--cut_nc'</code>
<code proglang="python">domE == 10.0 and model_specific != '--cut_ga' and model_specific != '--cut_nc'</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " --domT $value" : ""</code>
<code proglang="python">( "" , " --domT " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">Instead of thresholding per-domain output on E-value, instead report domains with
a bit score of >= value.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>thresholds_output</name>
<prompt lang="en">Options controlling inclusion (significance) thresholds.</prompt>
<argpos>1</argpos>
<comment>
<text lang="en">'Inclusion' thresholds are stricter than reporting thresholds. Inclusion thresholds
control which hits are considered to be reliable enough to be included in an output alignment or a
subsequent search round. In hmmscan, which does not have any alignment output nor any iterative
search steps, inclusion thresholds have little effect. They only affect what domains get
marked as significant ('!') or questionable ('?') in domain output.</text>
</comment>
<parameters>
<parameter>
<name>incE</name>
<prompt lang="en">Include sequences lower than this E-value threshold in output alignment (--incE)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">not defined $incT and $model_specific ne '--cut_ga' </code>
<code proglang="python">incT is None and model_specific != '--cut_ga' </code>
</precond>
<vdef>
<value>0.01</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != vdef) ? " --incE $value" : ""</code>
<code proglang="python">( "" , " --incE " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Use an E-value of <= value as the per-target inclusion threshold. The default is
0.01, meaning that on average, about 1 false positive would be expected in every
100 searches with different query sequences.</text>
</comment>
</parameter>
<parameter>
<name>incdomE</name>
<prompt lang="en">Include domains lower than this E-value threshold in output alignment (--incdomE)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">defined $incdomT and not defined model_specific</code>
<code proglang="python">incdomT is not None and model_specific is None</code>
</precond>
<vdef>
<value>0.01</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != vdef) ? " --incdomE $value" : ""</code>
<code proglang="python">( "" , " --incdomE " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Use a conditional E-value of <= value as the per-domain inclusion threshold, in
targets that have already satisfied the overall per-target inclusion threshold. The
default is 0.01.</text>
</comment>
</parameter>
<parameter>
<name>incT</name>
<prompt lang="en">Include sequences upper than this score threshold in output alignment (--incT)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$incE == 0.01 and $model_specific ne '--cut_ga'</code>
<code proglang="python">incE == 0.01 and model_specific != '--cut_ga'</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " --incT $value" : ""</code>
<code proglang="python">( "" , " --incT " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">Instead of using E-values for setting the inclusion threshold, instead use a bit score
of >= the value as the per-target inclusion threshold. It would be unusual to use bit
score thresholds with hmmscan, because you don't expect a single score threshold
to work for different profiles; different profiles have slightly different expected score
distributions.</text>
</comment>
</parameter>
<parameter>
<name>incdomT</name>
<prompt lang="en">Include domans upper than this score threshold in output alignment (--incdomT)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$incdomE == 0.01 and not defined $model_specific </code>
<code proglang="python">incdomE == 0.01 and model_specific is None</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " --incdomT $value" : ""</code>
<code proglang="python">( "" , " --incdomT " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">Instead of using E-values, instead use a bit score of >= value as the per-domain
inclusion threshold. As with --incT above, it would be unusual to use a single bit
score threshold in hmmscan.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<parameter>
<name>model_specific</name>
<prompt lang="en">Options controlling model-specific thresholding</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">not defined $Bit_cutoff and not $E_value_cutoff == 10.0 and not defined $incdomT and $incdomE == 0.01</code>
<code proglang="python">not Bit_cutoff and E_value_cutoff == 10.0 and incdomT is None and incdomE == 0.01</code>
</precond>
<vdef>
<value>null</value>
</vdef>
<vlist>
<velem undef="1">
<value>null</value>
<label>No profile</label>
</velem>
<velem>
<value>--cut_ga</value>
<label>use profile's GA gathering cutoffs</label>
</velem>
<velem>
<value>--cut_nc</value>
<label>use profile's NC noise cutoffs</label>
</velem>
<velem>
<value>--cut_tc</value>
<label>use profile's TC trusted cutoffs</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">Curated profile databases may define specific bit score thresholds for each profile, superseding any thresholding
based on statistical significance alone. To use these options, the profile must contain the appropriate
(GA, TC, and/or NC) optional score threshold annotation; this is picked up by hmmbuild from Stockholm
format alignment files. Each thresholding option has two scores: the per-sequence threshold x1 value and the
per-domain threshold x2 value. These act as if -T x1 --incT x1 --domT x2 --incdomT x2 has been
applied specifically using each model's curated thresholds.</text>
<text lang="en">cut ga: Use the GA (gathering) bit scores in the model to set per-sequence (GA1) and
per-domain (GA2) reporting and inclusion thresholds. GA thresholds are generally
considered to be the reliable curated thresholds defining family membership; for
example, in Pfam, these thresholds define what gets included in Pfam Full alignments
based on searches with Pfam Seed models.</text>
<text lang="en">cut_nc: Use the NC (noise cutoff) bit score thresholds in the model to set per-sequence
(NC1) and per-domain (NC2) reporting and inclusion thresholds. NC thresholds
are generally considered to be the score of the highest-scoring known false positive.</text>
<text lang="en">cut_tc: Use the NC (trusted cutoff) bit score thresholds in the model to set per-sequence
(TC1) and per-domain (TC2) reporting and inclusion thresholds. TC thresholds are
generally considered to be the score of the lowest-scoring known true positive that
is above all known false positives.</text>
</comment>
</parameter>
<paragraph>
<name>acceleration</name>
<prompt lang="en">Options controlling acceleration heuristics</prompt>
<argpos>1</argpos>
<comment>
<text lang="en">HMMER3 searches are accelerated in a three-step filter pipeline: the MSV filter, the Viterbi filter, and
the Forward filter. The first filter is the fastest and most approximate; the last is the full Forward scoring
algorithm. There is also a 'bias filter' step between MSV and Viterbi. Targets that pass all the steps
in the acceleration pipeline are then subjected to 'postprocessing' -- domain identification and scoring
using the Forward/Backward algorithm. Changing filter thresholds only removes or includes targets from
consideration; changing filter thresholds does not alter bit scores, E-values, or alignments, all of which are
determined solely in 'postprocessing'.</text>
</comment>
<parameters>
<parameter>
<name>max</name>
<prompt lang="en">Turn all heuristic filters off (less speed, more power) (--max)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " --max" : ""</code>
<code proglang="python">( "" , " --max " )[ value ]</code>
</format>
<comment>
<text lang="en">Turn off all filters, including the bias filter, and run full Forward/Backward postprocessing
on every target. This increases sensitivity somewhat, at a large cost in speed.</text>
</comment>
</parameter>
<parameter>
<name>F1</name>
<prompt lang="en">Stage 1 (MSV) threshold</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $max</code>
<code proglang="python">not max</code>
</precond>
<vdef>
<value>0.02</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef ) ? " --F1 $value" : ""</code>
<code proglang="python">( "" , " --F1 " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Set the P-value threshold for the MSV filter step. The default is 0.02, meaning that
roughly 2% of the highest scoring nonhomologous targets are expected to pass the filter.</text>
</comment>
</parameter>
<parameter>
<name>F2</name>
<prompt lang="en">Stage 1 (Vit) threshold</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $max</code>
<code proglang="python">not max</code>
</precond>
<vdef>
<value>0.001</value>
</vdef>
<format>
<code proglang="perl">( defined $value and $value != $vdef ) ? " --F2 $value" : ""</code>
<code proglang="python">( "" , " --F2 " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Set the P-value threshold for the Viterbi filter step. The default is 0.001.</text>
</comment>
</parameter>
<parameter>
<name>F3</name>
<prompt lang="en">Stage 1 (Fwd) threshold</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $max</code>
<code proglang="python">not max</code>
</precond>
<vdef>
<value>0.00001</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef ) ? " --F3 $value" : ""</code>
<code proglang="python">( "" , " --F3 " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Set the P-value threshold for the Forward filter step. The default is 1e-5.</text>
</comment>
</parameter>
<parameter>
<name>nobias</name>
<prompt lang="en">Turn off composition bias filter (--nobias)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $max</code>
<code proglang="python">not max</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " --nobias" : ""</code>
<code proglang="python">( "" , " --nobias " )[ value ]</code>
</format>
<comment>
<text lang="en">Turn off the bias filter. This increases sensitivity somewhat, but can come at a
high cost in speed, especially if the query has biased residue composition (such
as a repetitive sequence region, or if it is a membrane protein with large regions
of hydrophobicity). Without the bias filter, too many sequences may pass the filter
with biased queries, leading to slower than expected performance as the computationally
intensive Forward/Backward algorithms shoulder an abnormally heavy
load.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>expert</name>
<prompt lang="en">Other expert options</prompt>
<argpos>1</argpos>
<parameters>
<parameter>
<name>nonull2</name>
<prompt lang="en">Turn off biased composition score corrections (--nonull2)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " --nonull2" : ""</code>
<code proglang="python">( "" , " --nonull2 " )[ value ]</code>
</format>
<comment>
<text lang="en">Turn off the 'null2' score corrections for biased composition.</text>
</comment>
</parameter>
<parameter>
<name>E_value_calculation</name>
<prompt lang="en">Control of E_value calculation (-Z)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -Z $value" : ""</code>
<code proglang="python">( "" , " -Z " + str(value) )[ value is not None ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Assert that the total number of targets in your searches is the value, for the purposes of
per-sequence E-value calculations, rather than the actual number of targets seen.</text>
</comment>
</parameter>
<parameter>
<name>domZ</name>
<prompt lang="en">Set Z score of significant sequences, for domain E-value calculation (--domZ)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " --domZ $value" : ""</code>
<code proglang="python">( "" , " --domZ " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">Assert that the total number of targets in your searches is the value, for the purposes
of per-domain conditional E-value calculations, rather than the number of targets
that passed the reporting thresholds.</text>
</comment>
</parameter>
<parameter>
<name>seed</name>
<prompt lang="en">Set RNG seed number (--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">Set the random number seed to value. Some steps in postprocessing require Monte
Carlo simulation. The default is to use a fixed seed (42), so that results are exactly
reproducible. Any other positive integer will give different (but also reproducible)
results. A choice of 0 uses a 'randomly chosen' seed.</text>
</comment>
<ctrl>
<message>
<text lang="en">Enter a value >= 0</text>
</message>
<code proglang="perl">0 <= $value</code>
<code proglang="python">0 <= value</code>
</ctrl>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>output_options</name>
<prompt lang="en">Options directing output</prompt>
<argpos>1</argpos>
<parameters>
<parameter>
<name>textw</name>
<prompt lang="en">Set max width of ASCII text output lines (--textw)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>120</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " --textw $value " : ""</code>
<code proglang="python">( "" , " --textw " + str(value) )[ value is not None and value !=vdef ]</code>
</format>
<comment>
<text lang="en">Set the main output's line length limit to value> characters per line. The default is
120.</text>
</comment>
</parameter>
<parameter>
<name>notextw</name>
<prompt lang="en">Unlimit ASCII text output line width (--notextw)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">$textw == 120</code>
<code proglang="python">textw == 120</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " --notextw " : ""</code>
<code proglang="python">( "" , " --notextw " )[ value ]</code>
</format>
<comment>
<text lang="en">Unlimit the length of each line in the main output. The default is a limit of 120
characters per line, which helps in displaying the output cleanly on terminals and
in editors, but can truncate target profile description lines.</text>
</comment>
</parameter>
<parameter>
<name>acc</name>
<prompt lang="en">Prefer accessions over names in output (--acc)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " --acc " : ""</code>
<code proglang="python">( "" , " --acc " )[ value ]</code>
</format>
<comment>
<text lang="en">Use accessions instead of names in the main output, where available for profiles
and/or sequences</text>
</comment>
</parameter>
<parameter>
<name>outfile_name</name>
<prompt lang="en">Name of the sequence(s) file (-o)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -o $value" : ""</code>
<code proglang="python">( " " , " -o " + str(value) )[ value is not None ]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter isout="1">
<name>output_file_name</name>
<prompt lang="en">Output file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<precond>
<code proglang="perl">$outfile_name</code>
<code proglang="python">outfile_name</code>
</precond>
<filenames>
<code proglang="perl">$outfile_name</code>
<code proglang="python">str(outfile_name)</code>
</filenames>
</parameter>
<parameter>
<name>noali</name>
<prompt lang="en">Don't output alignments, so output is smaller (--noali)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">( $value ) ? " --noali " : ""</code>
<code proglang="python">( "" , " --noali " )[ value ]</code>
</format>
<comment>
<text lang="en">Omit the alignment section from the main output. This can greatly reduce the
output volume.</text>
</comment>
</parameter>
<parameter>
<name>alnfile_name</name>
<prompt lang="en">File name of the multiple alignment of all hits (-A)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -A $value" : ""</code>
<code proglang="python">( "" , " -A " + str(value) )[ value is not None ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Save a multiple alignment of all significant hits (those satisfying inclusion thresholds)
to the file.</text>
</comment>
</parameter>
<parameter isout="1">
<name>output_align_name</name>
<prompt lang="en">Output align file</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>STOCKHOLM</dataFormat>
</type>
<precond>
<code proglang="perl">$alnfile_name</code>
<code proglang="python">alnfile_name</code>
</precond>
<filenames>
<code proglang="perl">"$alnfile_name"</code>
<code proglang="python">str(alnfile_name)</code>
</filenames>
</parameter>
<parameter>
<name>perseqfile_name</name>
<prompt lang="en">File name of parseable table of per-sequence hits (--tblout)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " --tblout $value" : ""</code>
<code proglang="python">( "" , " --tblout " + str(value) )[ value is not None ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Save a simple tabular (space-delimited) file summarizing the 'per-target' output,
with one data line per homologous target model found</text>
</comment>
</parameter>
<parameter isout="1">
<name>output_perseqfile_name</name>
<prompt lang="en">Output parseable table of per-sequence hits</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<precond>
<code proglang="perl">$perseqfile_name</code>
<code proglang="python">perseqfile_name</code>
</precond>
<filenames>
<code proglang="perl">"$perseqfile_name"</code>
<code proglang="python">str(perseqfile_name)</code>
</filenames>
</parameter>
<parameter>
<name>perdomfile_name</name>
<prompt lang="en">File name of parseable table of per-domain hits (--domtblout)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " --domtblout $value" : ""</code>
<code proglang="python">( "" , " --domtblout " + str(value) )[ value is not None ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Save a simple tabular (space-delimited) file summarizing the 'per-domain' output,
with one data line per homologous domain detected in a query sequence for each
homologous model.</text>
</comment>
</parameter>
<parameter isout="1">
<name>output_perdomfile_name</name>
<prompt lang="en">Output parseable table of per-domain hits</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<precond>
<code proglang="perl">$perdomfile_name</code>
<code proglang="python">perdomfile_name</code>
</precond>
<filenames>
<code proglang="perl">"$perdomfile_name"</code>
<code proglang="python">str(perdomfile_name)</code>
</filenames>
</parameter>
</parameters>
</paragraph>
</parameters>
</program>
|