/var/lib/mobyle/programs/showalign.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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 | <?xml version="1.0" encoding="ISO-8859-1"?>
<!-- XML Authors: Corinne Maufrais and Nicolas Joly, -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>showalign</name>
<package>
<name>EMBOSS</name>
<version>6.3.1</version>
<doc>
<title>EMBOSS</title>
<description>
<text lang="en">European Molecular Biology Open Software Suite</text>
</description>
<authors>Rice,P. Longden,I. and Bleasby, A.</authors>
<reference>EMBOSS: The European Molecular Biology Open Software Suite (2000) Rice,P. Longden,I. and Bleasby, A. Trends in Genetics 16, (6) pp276--277</reference>
<sourcelink>http://emboss.sourceforge.net/download</sourcelink>
<homepagelink>http://emboss.sourceforge.net</homepagelink>
</doc>
</package>
<doc>
<title>showalign</title>
<description>
<text lang="en">Display a multiple sequence alignment in pretty format</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/showalign.html</doclink>
<doclink>http://emboss.sourceforge.net/docs/themes</doclink>
</doc>
<category>alignment:multiple:display</category>
<command>showalign</command>
</head>
<parameters>
<paragraph>
<name>e_input</name>
<prompt lang="en">Input section</prompt>
<parameters>
<parameter issimple="1" ismandatory="1">
<name>e_sequence</name>
<prompt lang="en">sequence option</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>FASTA</dataFormat>
<dataFormat>MSF</dataFormat>
<dataFormat>PAIR</dataFormat>
<dataFormat>MARKX0</dataFormat>
<dataFormat>MARKX1</dataFormat>
<dataFormat>MARKX2</dataFormat>
<dataFormat>MARKX3</dataFormat>
<dataFormat>MARKX10</dataFormat>
<dataFormat>SRS</dataFormat>
<dataFormat>SRSPAIR</dataFormat>
<dataFormat>SCORE</dataFormat>
<dataFormat>UNKNOWN</dataFormat>
<dataFormat>MULTIPLE</dataFormat>
<dataFormat>SIMPLE</dataFormat>
<dataFormat>MATCH</dataFormat>
<card>1,n</card>
</type>
<format>
<code proglang="python">("", " -sequence=" + str(value))[value is not None]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">The sequence alignment to be displayed.</text>
</comment>
</parameter>
<parameter>
<name>e_matrix</name>
<prompt lang="en">Similarity scoring matrix file</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>mobyle_null</value>
</vdef>
<vlist>
<velem undef="1">
<value>mobyle_null</value>
<label></label>
</velem>
<velem>
<value>EBLOSUM30</value>
<label>Eblosum30</label>
</velem>
<velem>
<value>EBLOSUM35</value>
<label>Eblosum35</label>
</velem>
<velem>
<value>EBLOSUM40</value>
<label>Eblosum40</label>
</velem>
<velem>
<value>EBLOSUM45</value>
<label>Eblosum45</label>
</velem>
<velem>
<value>EBLOSUM50</value>
<label>Eblosum50</label>
</velem>
<velem>
<value>EBLOSUM55</value>
<label>Eblosum55</label>
</velem>
<velem>
<value>EBLOSUM60</value>
<label>Eblosum60</label>
</velem>
<velem>
<value>EBLOSUM62</value>
<label>Eblosum62</label>
</velem>
<velem>
<value>EBLOSUM62-12</value>
<label>Eblosum62-12</label>
</velem>
<velem>
<value>EBLOSUM65</value>
<label>Eblosum65</label>
</velem>
<velem>
<value>EBLOSUM70</value>
<label>Eblosum70</label>
</velem>
<velem>
<value>EBLOSUM75</value>
<label>Eblosum75</label>
</velem>
<velem>
<value>EBLOSUM80</value>
<label>Eblosum80</label>
</velem>
<velem>
<value>EBLOSUM85</value>
<label>Eblosum85</label>
</velem>
<velem>
<value>EBLOSUM90</value>
<label>Eblosum90</label>
</velem>
<velem>
<value>EBLOSUMN</value>
<label>Eblosumn</label>
</velem>
<velem>
<value>EDNAFULL</value>
<label>Ednafull</label>
</velem>
<velem>
<value>EDNAMAT</value>
<label>Ednamat</label>
</velem>
<velem>
<value>EDNASIMPLE</value>
<label>Ednasimple</label>
</velem>
<velem>
<value>EPAM10</value>
<label>Epam10</label>
</velem>
<velem>
<value>EPAM100</value>
<label>Epam100</label>
</velem>
<velem>
<value>EPAM110</value>
<label>Epam110</label>
</velem>
<velem>
<value>EPAM120</value>
<label>Epam120</label>
</velem>
<velem>
<value>EPAM130</value>
<label>Epam130</label>
</velem>
<velem>
<value>EPAM140</value>
<label>Epam140</label>
</velem>
<velem>
<value>EPAM150</value>
<label>Epam150</label>
</velem>
<velem>
<value>EPAM160</value>
<label>Epam160</label>
</velem>
<velem>
<value>EPAM170</value>
<label>Epam170</label>
</velem>
<velem>
<value>EPAM180</value>
<label>Epam180</label>
</velem>
<velem>
<value>EPAM190</value>
<label>Epam190</label>
</velem>
<velem>
<value>EPAM20</value>
<label>Epam20</label>
</velem>
<velem>
<value>EPAM200</value>
<label>Epam200</label>
</velem>
<velem>
<value>EPAM210</value>
<label>Epam210</label>
</velem>
<velem>
<value>EPAM220</value>
<label>Epam220</label>
</velem>
<velem>
<value>EPAM230</value>
<label>Epam230</label>
</velem>
<velem>
<value>EPAM240</value>
<label>Epam240</label>
</velem>
<velem>
<value>EPAM250</value>
<label>Epam250</label>
</velem>
<velem>
<value>EPAM260</value>
<label>Epam260</label>
</velem>
<velem>
<value>EPAM270</value>
<label>Epam270</label>
</velem>
<velem>
<value>EPAM280</value>
<label>Epam280</label>
</velem>
<velem>
<value>EPAM290</value>
<label>Epam290</label>
</velem>
<velem>
<value>EPAM30</value>
<label>Epam30</label>
</velem>
<velem>
<value>EPAM300</value>
<label>Epam300</label>
</velem>
<velem>
<value>EPAM310</value>
<label>Epam310</label>
</velem>
<velem>
<value>EPAM320</value>
<label>Epam320</label>
</velem>
<velem>
<value>EPAM330</value>
<label>Epam330</label>
</velem>
<velem>
<value>EPAM340</value>
<label>Epam340</label>
</velem>
<velem>
<value>EPAM350</value>
<label>Epam350</label>
</velem>
<velem>
<value>EPAM360</value>
<label>Epam360</label>
</velem>
<velem>
<value>EPAM370</value>
<label>Epam370</label>
</velem>
<velem>
<value>EPAM380</value>
<label>Epam380</label>
</velem>
<velem>
<value>EPAM390</value>
<label>Epam390</label>
</velem>
<velem>
<value>EPAM40</value>
<label>Epam40</label>
</velem>
<velem>
<value>EPAM400</value>
<label>Epam400</label>
</velem>
<velem>
<value>EPAM410</value>
<label>Epam410</label>
</velem>
<velem>
<value>EPAM420</value>
<label>Epam420</label>
</velem>
<velem>
<value>EPAM430</value>
<label>Epam430</label>
</velem>
<velem>
<value>EPAM440</value>
<label>Epam440</label>
</velem>
<velem>
<value>EPAM450</value>
<label>Epam450</label>
</velem>
<velem>
<value>EPAM460</value>
<label>Epam460</label>
</velem>
<velem>
<value>EPAM470</value>
<label>Epam470</label>
</velem>
<velem>
<value>EPAM480</value>
<label>Epam480</label>
</velem>
<velem>
<value>EPAM490</value>
<label>Epam490</label>
</velem>
<velem>
<value>EPAM50</value>
<label>Epam50</label>
</velem>
<velem>
<value>EPAM500</value>
<label>Epam500</label>
</velem>
<velem>
<value>EPAM60</value>
<label>Epam60</label>
</velem>
<velem>
<value>EPAM70</value>
<label>Epam70</label>
</velem>
<velem>
<value>EPAM80</value>
<label>Epam80</label>
</velem>
<velem>
<value>EPAM90</value>
<label>Epam90</label>
</velem>
<velem>
<value>SSSUB</value>
<label>Sssub</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -matrix=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_additional</name>
<prompt lang="en">Additional section</prompt>
<parameters>
<parameter>
<name>e_refseq</name>
<prompt lang="en">The number or the name of the reference sequence</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -refseq=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>3</argpos>
<comment>
<text lang="en">If you give the number in the alignment or the name of a sequence, it will be taken to be the reference sequence. The reference sequence is always shown in full and is the one against which all the other sequences are compared. If this is set to 0 then the consensus sequence will be used as the reference sequence. By default the consensus sequence is used as the reference sequence.</text>
</comment>
</parameter>
<parameter>
<name>e_bottom</name>
<prompt lang="en">Display the reference sequence at the bottom</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nobottom", "")[ bool(value) ]</code>
</format>
<argpos>4</argpos>
<comment>
<text lang="en">If this is true then the reference sequence is displayed at the bottom of the alignment instead of the top.</text>
</comment>
</parameter>
<parameter>
<name>e_show</name>
<prompt lang="en">What to show</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>N</value>
</vdef>
<vlist>
<velem>
<value>A</value>
<label>All of the sequences</label>
</velem>
<velem>
<value>I</value>
<label>Identities between the sequences</label>
</velem>
<velem>
<value>N</value>
<label>Non-identities between the sequences</label>
</velem>
<velem>
<value>S</value>
<label>Similarities between the sequences</label>
</velem>
<velem>
<value>D</value>
<label>Dissimilarities between the sequences</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -show=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>5</argpos>
</parameter>
<parameter>
<name>e_order</name>
<prompt lang="en">Output order of the sequences</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>I</value>
</vdef>
<vlist>
<velem>
<value>I</value>
<label>Input order - no change</label>
</velem>
<velem>
<value>A</value>
<label>Alphabetical order of the names</label>
</velem>
<velem>
<value>S</value>
<label>Similarity to the reference sequence</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -order=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>6</argpos>
</parameter>
<parameter>
<name>e_similarcase</name>
<prompt lang="en">Show similar residues in lower-case</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nosimilarcase", "")[ bool(value) ]</code>
</format>
<argpos>7</argpos>
<comment>
<text lang="en">If this is set True, then when -show is set to 'Similarities' or 'Non-identities' and a residue is similar but not identical to the reference sequence residue, it will be changed to lower-case. If -show is set to 'All' then non-identical, non-similar residues will be changed to lower-case. If this is False then no change to the case of the residues is made on the basis of their similarity to the reference sequence.</text>
</comment>
</parameter>
<parameter>
<name>e_consensus</name>
<prompt lang="en">Display the consensus line</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -noconsensus", "")[ bool(value) ]</code>
</format>
<argpos>8</argpos>
<comment>
<text lang="en">If this is true then the consensus line is displayed.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_advanced</name>
<prompt lang="en">Advanced section</prompt>
<parameters>
<parameter>
<name>e_uppercase</name>
<prompt lang="en">Regions to put in uppercase (eg: 4-57,78-94)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">("", " -uppercase=" + str(value))[value is not None]</code>
</format>
<argpos>9</argpos>
<comment>
<text lang="en">Regions to put in uppercase.
If this is left blank, then the sequence case is left alone.
A set of regions is specified by a set of pairs of positions.
The positions are integers.
They are separated by any non-digit, non-alpha character.
Examples of region specifications are:
24-45, 56-78
1:45, 67=99;765..888
1,5,8,10,23,45,57,99</text>
</comment>
</parameter>
<parameter>
<name>e_number</name>
<prompt lang="en">Number the sequences</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nonumber", "")[ bool(value) ]</code>
</format>
<argpos>10</argpos>
<comment>
<text lang="en">If this option is true then a line giving the positions in the alignment is displayed every 10 characters above the alignment.</text>
</comment>
</parameter>
<parameter>
<name>e_ruler</name>
<prompt lang="en">Display ruler</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -noruler", "")[ bool(value) ]</code>
</format>
<argpos>11</argpos>
<comment>
<text lang="en">If this option is true then a ruler line marking every 5th and 10th character in the alignment is displayed.</text>
</comment>
</parameter>
<parameter>
<name>e_width</name>
<prompt lang="en">Width of sequence to display (value greater than or equal to 1)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>60</value>
</vdef>
<format>
<code proglang="python">("", " -width=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 1 is required</text>
</message>
<code proglang="python">value >= 1</code>
</ctrl>
<argpos>12</argpos>
</parameter>
<parameter>
<name>e_margin</name>
<prompt lang="en">Length of margin for sequence names (value greater than or equal to -1)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>-1</value>
</vdef>
<format>
<code proglang="python">("", " -margin=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to -1 is required</text>
</message>
<code proglang="python">value >= -1</code>
</ctrl>
<argpos>13</argpos>
<comment>
<text lang="en">This sets the length of the left-hand margin for sequence names. If the margin is set at 0 then no margin and no names are displayed. If the margin is set to a value that is less than the length of a sequence name then the sequence name is displayed truncated to the length of the margin. If the margin is set to -1 then the minimum margin width that will allow all the sequence names to be displayed in full plus a space at the end of the name will automatically be selected.</text>
</comment>
</parameter>
<parameter>
<name>e_html</name>
<prompt lang="en">Use html formatting</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -html")[ bool(value) ]</code>
</format>
<argpos>14</argpos>
</parameter>
<parameter>
<name>e_highlight</name>
<prompt lang="en">Regions to colour in html (eg: 4-57 red 78-94 green)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">("", " -highlight=" + str(value))[value is not None]</code>
</format>
<argpos>15</argpos>
<comment>
<text lang="en">Regions to colour if formatting for HTML.
If this is left blank, then the sequence is left alone.
A set of regions is specified by a set of pairs of positions.
The positions are integers.
They are followed by any valid HTML font colour.
Examples of region specifications are:
24-45 blue 56-78 orange
1-100 green 120-156 red
A file of ranges to colour (one range per line) can be specified as '@filename'.</text>
</comment>
</parameter>
<parameter>
<name>e_plurality</name>
<prompt lang="en">Plurality check % for consensus (value from 0.0 to 100.0)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>50.0</value>
</vdef>
<format>
<code proglang="python">("", " -plurality=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 0.0 is required</text>
</message>
<code proglang="python">value >= 0.0</code>
</ctrl>
<ctrl>
<message>
<text lang="en">Value less than or equal to 100.0 is required</text>
</message>
<code proglang="python">value <= 100.0</code>
</ctrl>
<argpos>16</argpos>
<comment>
<text lang="en">Set a cut-off for the % of positive scoring matches below which there is no consensus. The default plurality is taken as 50% of the total weight of all the sequences in the alignment.</text>
</comment>
</parameter>
<parameter>
<name>e_setcase</name>
<prompt lang="en">Threshold above which the consensus is given in uppercase</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="python">("", " -setcase=" + str(value))[value is not None]</code>
</format>
<argpos>17</argpos>
<comment>
<text lang="en">Sets the threshold for the scores of the positive matches above which the consensus is in upper-case and below which the consensus is in lower-case. By default this is set to be half of the (weight-adjusted) number of sequences in the alignment.</text>
</comment>
</parameter>
<parameter>
<name>e_identity</name>
<prompt lang="en">Required % of identities at a position for consensus (value from 0.0 to 100.0)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.0</value>
</vdef>
<format>
<code proglang="python">("", " -identity=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 0.0 is required</text>
</message>
<code proglang="python">value >= 0.0</code>
</ctrl>
<ctrl>
<message>
<text lang="en">Value less than or equal to 100.0 is required</text>
</message>
<code proglang="python">value <= 100.0</code>
</ctrl>
<argpos>18</argpos>
<comment>
<text lang="en">Provides the facility of setting the required number of identities at a position for it to give a consensus. Therefore, if this is set to 100% only columns of identities contribute to the consensus.</text>
</comment>
</parameter>
<parameter>
<name>e_gaps</name>
<prompt lang="en">Use gap characters in consensus</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nogaps", "")[ bool(value) ]</code>
</format>
<argpos>19</argpos>
<comment>
<text lang="en">If this option is true then gap characters can appear in the consensus. The alternative is 'N' for nucleotide, or 'X' for protein</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_output</name>
<prompt lang="en">Output section</prompt>
<parameters>
<parameter>
<name>e_outfile</name>
<prompt lang="en">Name of the output file (e_outfile)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<vdef>
<value>showalign.e_outfile</value>
</vdef>
<format>
<code proglang="python">("" , " -outfile=" + str(value))[value is not None]</code>
</format>
<argpos>20</argpos>
</parameter>
<parameter isout="1">
<name>e_outfile_out</name>
<prompt lang="en">outfile_out option</prompt>
<type>
<datatype>
<class>ShowalignReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<filenames>
<code proglang="python">e_outfile</code>
</filenames>
</parameter>
</parameters>
</paragraph>
<parameter ishidden="1">
<name>auto</name>
<prompt lang="en">Turn off any prompting</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">" -auto -stdout"</code>
</format>
<argpos>21</argpos>
</parameter>
</parameters>
</program>
|