/var/lib/mobyle/programs/psiblast.xml is in mobyle-programs 5.1.1-1.
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 | <?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>psiblast</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/blast_package.xml"/>
<doc>
<title>PSI-Blast</title>
<description>
<text lang="en">Position Specific Iterative Blast</text>
</description>
<reference>Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaeffer,Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402.</reference>
</doc>
<category>database:search:homology</category>
<category>database:search:pattern</category>
</head>
<parameters xmlns:xi="http://www.w3.org/2001/XInclude">
<parameter iscommand="1" ishidden="1">
<name>psiblast</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"blastpgp"</code>
<code proglang="python">"blastpgp"</code>
</format>
<argpos>0</argpos>
<comment>
<text lang="en">The blastpgp program can do an iterative search in which sequences found in one round of searching are used to build a score model for the next round of searching. In this usage, the program is called Position-Specific Iterated BLAST, or PSI-BLAST. As explained in the accompanying paper, the BLAST algorithm is not tied to a specific score matrix. Traditionally, it has been implemented using an AxA substitution matrix where A is the alphabet size. PSI-BLAST instead uses a QxA matrix, where Q is the length of the query sequence; at each position the cost of a letter depends on the position w.r.t. the query and the letter in the subject sequence.</text>
<text lang="en">The position-specific matrix for round i+1 is built from a constrained multiple alignment among the query and the sequences found with sufficiently low e-value in round i. The top part of the output for each round distinguishes the sequences into: sequences found previously and used in the score model, and sequences not used in the score model. The output currently includes lots of diagnostics requested by users at NCBI. To skip quickly from the output of one round to the next, search for the string 'producing', which is part of the header for each round and likely does not appear elsewhere in the output. PSI-BLAST 'converges' and stops if all sequences found at round i+1 below the e-value threshold were already in the model at the beginning of the round.</text>
</comment>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>query</name>
<prompt lang="en">Sequence File (-i)</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<format>
<code proglang="perl">" -i $query" </code>
<code proglang="python">" -i " + str(value)</code>
</format>
<argpos>3</argpos>
</parameter>
<parameter>
<name>start_region</name>
<prompt lang="en">Start of required region in query (-S)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -S $value" : ""</code>
<code proglang="python">( "" , " -S " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>end_region</name>
<prompt lang="en">End of required region in query (-H)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>-1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -H $value" : ""</code>
<code proglang="python">( "" , " -H " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Location on query sequence. -1 indicates end of query</text>
</comment>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>protein_db</name>
<prompt lang="en">Protein database (-d )</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<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"> " -d $value" </code>
<code proglang="python"> " -d " + str(value) </code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">Choose a protein db for blastp or blastx.</text>
</comment>
</parameter>
<paragraph>
<name>scoring</name>
<prompt lang="en">Scoring option</prompt>
<argpos>4</argpos>
<parameters>
<parameter>
<name>open_a_gap</name>
<prompt lang="en">Cost to open a gap (-G)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>11</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -G $value" : ""</code>
<code proglang="python">( "" , " -G " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>extend_a_gap</name>
<prompt lang="en">Cost to extend a gap (-E)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</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>
<comment>
<text lang="en">Limited values for gap existence and extension are supported for these three programs. Some supported and suggested values are:</text>
<text lang="en">Existence Extension</text>
<text lang="en">10 -- 1</text>
<text lang="en">10 -- 2</text>
<text lang="en">11 -- 1</text>
<text lang="en">8 -- 2</text>
<text lang="en">9 -- 2</text>
<text lang="en">(source: NCBI Blast page)</text>
</comment>
</parameter>
<parameter>
<name>matrix</name>
<prompt lang="en">Similarity matrix (-M)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>BLOSUM62</value>
</vdef>
<vlist>
<velem>
<value>BLOSUM45</value>
<label>BLOSUM45</label>
</velem>
<velem>
<value>BLOSUM80</value>
<label>BLOSUM80</label>
</velem>
<velem>
<value>BLOSUM62</value>
<label>BLOSUM62</label>
</velem>
<velem>
<value>PAM30</value>
<label>PAM30</label>
</velem>
<velem>
<value>PAM70</value>
<label>PAM70</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " -M $value" : ""</code>
<code proglang="python">( "" , " -M " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>filter_opt</name>
<prompt lang="en">Filtering and masking options</prompt>
<argpos>5</argpos>
<comment>
<text lang="en">This options also takes a string as an argument. One may use such a string to change the specific parameters of seg or invoke other filters. Please see the 'Filtering Strings' section (below) for details.</text>
</comment>
<parameters>
<parameter>
<name>filter</name>
<prompt lang="en">Filter query sequence with SEG (-F)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -F T" : ""</code>
<code proglang="python">( "" , " -F T" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>lower_case</name>
<prompt lang="en">Use lower case filtering (-U)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -U T" : ""</code>
<code proglang="python">("", " -U T")[value]</code>
</format>
<comment>
<text lang="en">This option specifies that any lower-case letters in the input FASTA file should be masked.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>selectivity_opt</name>
<prompt lang="en">Selectivity options</prompt>
<argpos>5</argpos>
<parameters>
<parameter issimple="1">
<name>Expect</name>
<prompt lang="en">Expected value (-e)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>10</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>
<comment>
<text lang="en">The statistical significance threshold for reporting matches against database sequences; the default value is 10, such that 10 matches are expected to be found merely by chance, according to the stochastic model of Karlin and Altschul (1990). If the statistical significance ascribed to a match is greater than the EXPECT threshold, the match will not be reported. Lower EXPECT thresholds are more stringent, leading to fewer chance matches being reported. Fractional values are acceptable. </text>
</comment>
</parameter>
<parameter>
<name>word_size</name>
<prompt lang="en">Word Size (-W)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -W $value" : ""</code>
<code proglang="python">("" , " -W "+str(value))[value is not None]</code>
</format>
<ctrl>
<message>
<text lang="en">Valid wordsize range is 2 to 3</text>
</message>
<code proglang="perl">$value >= 2 and $value <=3</code>
<code proglang="python">value >= 2 and value <=3</code>
</ctrl>
<comment>
<text lang="en">Use words of size N.</text>
<text lang="en">Zero invokes default behavior</text>
<text lang="en">Default value: 3</text>
</comment>
</parameter>
<parameter>
<name>window</name>
<prompt lang="en">Multiple hits window size (-A)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>40</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -A $value" : ""</code>
<code proglang="python">( "" , " -A " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">When multiple hits method is used, this parameter defines the distance from last hit on the same diagonal to the new one.</text>
<text lang="en">Zero means single hit algorithm.</text>
</comment>
</parameter>
<parameter>
<name>extend_hit</name>
<prompt lang="en">Threshold for extending hits (-f)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>11</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -f $value" : ""</code>
<code proglang="python">( "" , " -f " + str(value) )[ value is not None and value !=vdef]</code>
</format>
<comment>
<text lang="en">Blast seeks first short word pairs whose aligned score reaches at least this value</text>
</comment>
</parameter>
<parameter>
<name>dropoff</name>
<prompt lang="en">X dropoff value for gapped alignment (-X)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -X $value":""</code>
<code proglang="python">("" , " -X " + str(value))[ value is not None ]</code>
</format>
<comment>
<text lang="en">This is the value that control the path graph region explored by Blast during a gapped extension (Xg in the NAR paper).</text>
</comment>
</parameter>
<parameter>
<name>dropoff_z</name>
<prompt lang="en">X dropoff value for final gapped alignment (-Z)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>25</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -Z $value" : ""</code>
<code proglang="python">( "" , " -Z " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">This parameter controls the dropoff for the final reported alignment. See also the -X parameter.</text>
</comment>
</parameter>
<parameter>
<name>dropoff_y</name>
<prompt lang="en">Dropoff for blast ungapped extensions in bits (-y)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>7.0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -y $value" : ""</code>
<code proglang="python">( "" , " -y " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">This parameter controls the dropoff at ungapped extension stage. See also the -X parameter.</text>
</comment>
</parameter>
<parameter>
<name>eff_len</name>
<prompt lang="en">Effective length of the search space (-Y)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -Y $value" : ""</code>
<code proglang="python">("" , " -Y "+str(value))[value is not None and value !=vdef]</code>
</format>
<comment>
<text lang="en">Use zero for the real size</text>
</comment>
</parameter>
<parameter>
<name>keep_hits</name>
<prompt lang="en">Number of best hits from a region to keep (-K)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -K $value" : ""</code>
<code proglang="python">("" , " -K "+str(value))[value is not None]</code>
</format>
<comment>
<text lang="en">If this option is used, a value of 100 is recommended.</text>
</comment>
</parameter>
<parameter>
<name>mode</name>
<prompt lang="en">Single-hit or multiple-hit mode (-P)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<vlist>
<velem>
<value>0</value>
<label>Multiple-hit (0)</label>
</velem>
<velem>
<value>1</value>
<label>Single-hit (1)</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value eq "0") ? " -P $value" : ""</code>
<code proglang="python">("" , " -P "+str(value))[value != "0"]</code>
</format>
</parameter>
<parameter>
<name>nb_bits</name>
<prompt lang="en">Number of bits to trigger gapping (-N)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>22</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -N $value" : ""</code>
<code proglang="python">("" , " -N "+str(value))[value is not None and value !=vdef]</code>
</format>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>psi_spec_opt</name>
<prompt lang="en">PSI-Blast specific selectivity options</prompt>
<argpos>5</argpos>
<parameters>
<parameter>
<name>max_passes</name>
<prompt lang="en">Maximum number of passes to use in multipass version (-j)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -j $value" : ""</code>
<code proglang="python">( "" , " -j " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>expect_in_multipass</name>
<prompt lang="en">e-value threshold for inclusion in multipass model (-h)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.002</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -h $value" : ""</code>
<code proglang="python">( "" , " -h " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>pseudocounts</name>
<prompt lang="en">Constant in pseudocounts for multipass version (-c)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>9</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -c $value" : ""</code>
<code proglang="python">( "" , " -c " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">This constant is the weight given to a pre-calculated residue target frequency (versus the observed one) in a column of the position specific matrix. The larger its value, the greater the emphasis given to prior knowledge of residue relationships vis a vis observed residue frequencies (beta constant in NAR paper).</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>affichage</name>
<prompt lang="en">Report options</prompt>
<argpos>5</argpos>
<parameters>
<parameter>
<name>Descriptions</name>
<prompt lang="en">Number of one-line descriptions to show? (-v)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>500</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -v $value" : ""</code>
<code proglang="python">( "" , " -v " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Maximum number of database sequences for which one-line descriptions will be reported.</text>
</comment>
</parameter>
<parameter>
<name>Alignments</name>
<prompt lang="en">Number of database sequences to show alignments? (-b)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>250</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -b $value" : ""</code>
<code proglang="python">( "" , " -b " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Maximum number of database sequences for which high-scoring segment pairs will be reported (-b).</text>
</comment>
</parameter>
<parameter>
<name>view_alignments</name>
<prompt lang="en">Alignment view options (-m)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<vlist>
<velem>
<value>0</value>
<label>Pairwise (0)</label>
</velem>
<velem>
<value>1</value>
<label>Query-anchored showing identities (1)</label>
</velem>
<velem>
<value>2</value>
<label>Query-anchored no identities (2)</label>
</velem>
<velem>
<value>3</value>
<label>Flat query-anchored, show identities (3)</label>
</velem>
<velem>
<value>4</value>
<label>Flat query-anchored, no identities (4)</label>
</velem>
<velem>
<value>5</value>
<label>Query-anchored no identities and blunt ends (5)</label>
</velem>
<velem>
<value>6</value>
<label>Flat query-anchored, no identities and blunt ends (6)</label>
</velem>
<velem>
<value>7</value>
<label>XML Blast output (7)</label>
</velem>
<velem>
<value>8</value>
<label>Tabular output (8)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " -m $value" : "" </code>
<code proglang="python">( "" , " -m " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter ishidden="1">
<name>txtoutput</name>
<prompt lang="en">Text output file</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="perl">$view_alignments ne "7"</code>
<code proglang="python">view_alignments != "7"</code>
</precond>
<format>
<code proglang="perl">" -o psiblast.txt"</code>
<code proglang="python">" -o psiblast.txt"</code>
</format>
<argpos>10</argpos>
</parameter>
<parameter ishidden="1">
<name>xmloutput</name>
<prompt lang="en">XML output file</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="perl">$view_alignments eq "7"</code>
<code proglang="python">view_alignments == "7"</code>
</precond>
<format>
<code proglang="perl">" -o psiblast.xml"</code>
<code proglang="python">" -o psiblast.xml"</code>
</format>
<argpos>10</argpos>
</parameter>
<parameter>
<name>htmloutput</name>
<prompt lang="en">Html output</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">$view_alignments !~ /^[78]$/</code>
<code proglang="python">view_alignments not in [ "7" , "8" ]</code>
</precond>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? " && html4blast -g -o psiblast.html psiblast.txt" : ""</code>
<code proglang="python">("" , " && html4blast -g -o psiblast.html psiblast.txt")[value]</code>
</format>
<argpos>11</argpos>
</parameter>
<parameter>
<name>believe</name>
<prompt lang="en">Believe the query defline (-J)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -J":""</code>
<code proglang="python">("" , " -J")[ value ]</code>
</format>
</parameter>
<parameter>
<name>seqalign_file</name>
<prompt lang="en">SeqAlign file (-J option must be true) (-O)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<precond>
<code proglang="perl">$believe</code>
<code proglang="python">believe</code>
</precond>
<format>
<code proglang="perl">(defined $value)? " -O $value" : ""</code>
<code proglang="python">( "" , " -O " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">SeqAlign is in ASN.1 format, so that it can be read with NCBI tools (such as sequin). This allows one to view the results in different formats.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>txtfile</name>
<prompt lang="en">Blast text report</prompt>
<type>
<datatype>
<class>BlastTextReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$view_alignments ne "7"</code>
<code proglang="python">view_alignments != "7"</code>
</precond>
<filenames>
<code proglang="perl">"psiblast.txt"</code>
<code proglang="python">"psiblast.txt"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>xmlfile</name>
<prompt lang="en">Blast xml report</prompt>
<type>
<datatype>
<class>BlastXmlReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$view_alignments eq "7"</code>
<code proglang="python">view_alignments == "7"</code>
</precond>
<filenames>
<code proglang="perl">"psiblast.xml"</code>
<code proglang="python">"psiblast.xml"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>htmlfile</name>
<prompt lang="en">Blast html report</prompt>
<type>
<datatype>
<class>BlastHtmlReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$view_alignments !~ /^[78]$/</code>
<code proglang="python">view_alignments not in ["7", "8"]</code>
</precond>
<filenames>
<code proglang="perl">"psiblast.html"</code>
<code proglang="python">"psiblast.html"</code>
</filenames>
</parameter>
<parameter isout="1" ishidden="1">
<name>imgfile</name>
<type>
<datatype>
<class>Picture</class>
<superclass>Binary</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$view_alignments !~ /^[78]$/</code>
<code proglang="python">view_alignments not in ["7", "8"]</code>
</precond>
<filenames>
<code proglang="perl">"*.png"</code>
<code proglang="perl">"*.gif"</code>
<code proglang="python">"*.png"</code>
<code proglang="python">"*.gif"</code>
</filenames>
</parameter>
<parameter>
<name>save_matrix</name>
<prompt lang="en">Save PSI-Blast Matrix to file (-C)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<precond>
<code proglang="perl">$max_passes > 1</code>
<code proglang="python">max_passes > 1</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -C $save_matrix" : ""</code>
<code proglang="python">( "" , " -C "+ str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>save_txt_matrix</name>
<prompt lang="en">Save PSI-BLAST Matrix as text to file (-Q)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<precond>
<code proglang="perl">$max_passes > 1</code>
<code proglang="python">max_passes > 1</code>
</precond>
<format>
<code proglang="perl">(defined $value)? " -Q $save_txt_matrix" : ""</code>
<code proglang="python">( "" , " -Q " + str(value) )[ value is not None ]</code>
</format>
</parameter>
</parameters>
</program>
|