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427 13.7 KB
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428 </div>
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430
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433 <div itemprop="text" class="blob-wrapper data type-xml">
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434 <table class="highlight tab-size js-file-line-container" data-tab-size="8">
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435 <tr>
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436 <td id="L1" class="blob-num js-line-number" data-line-number="1"></td>
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437 <td id="LC1" class="blob-code blob-code-inner js-file-line"><<span class="pl-ent">tool</span> <span class="pl-e">id</span>=<span class="pl-s"><span class="pl-pds">"</span>multiqc<span class="pl-pds">"</span></span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>multiqc<span class="pl-pds">"</span></span> <span class="pl-e">version</span>=<span class="pl-s"><span class="pl-pds">"</span>@WRAPPER_VERSION@.0<span class="pl-pds">"</span></span>></td>
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438 </tr>
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439 <tr>
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440 <td id="L2" class="blob-num js-line-number" data-line-number="2"></td>
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441 <td id="LC2" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">description</span>>aggregate results from bioinformatics analyses into a single report</<span class="pl-ent">description</span>></td>
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442 </tr>
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443 <tr>
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444 <td id="L3" class="blob-num js-line-number" data-line-number="3"></td>
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445 <td id="LC3" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">macros</span>></td>
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446 </tr>
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447 <tr>
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448 <td id="L4" class="blob-num js-line-number" data-line-number="4"></td>
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449 <td id="LC4" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">token</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>@WRAPPER_VERSION@<span class="pl-pds">"</span></span>>1.0.0</<span class="pl-ent">token</span>></td>
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450 </tr>
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451 <tr>
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452 <td id="L5" class="blob-num js-line-number" data-line-number="5"></td>
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453 <td id="LC5" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">macros</span>></td>
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454 </tr>
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455 <tr>
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456 <td id="L6" class="blob-num js-line-number" data-line-number="6"></td>
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457 <td id="LC6" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">requirements</span>></td>
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458 </tr>
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459 <tr>
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460 <td id="L7" class="blob-num js-line-number" data-line-number="7"></td>
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461 <td id="LC7" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">requirement</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>package<span class="pl-pds">"</span></span> <span class="pl-e">version</span>=<span class="pl-s"><span class="pl-pds">"</span>@WRAPPER_VERSION@<span class="pl-pds">"</span></span>>multiqc</<span class="pl-ent">requirement</span>></td>
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462 </tr>
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463 <tr>
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464 <td id="L8" class="blob-num js-line-number" data-line-number="8"></td>
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465 <td id="LC8" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">requirements</span>></td>
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466 </tr>
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467 <tr>
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468 <td id="L9" class="blob-num js-line-number" data-line-number="9"></td>
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469 <td id="LC9" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">version_command</span>>@WRAPPER_VERSION@</<span class="pl-ent">version_command</span>></td>
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470 </tr>
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471 <tr>
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472 <td id="L10" class="blob-num js-line-number" data-line-number="10"></td>
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473 <td id="LC10" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">command</span> <span class="pl-e">detect_errors</span>=<span class="pl-s"><span class="pl-pds">"</span>aggressive<span class="pl-pds">"</span></span>></td>
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474 </tr>
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475 <tr>
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476 <td id="L11" class="blob-num js-line-number" data-line-number="11"></td>
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477 <td id="LC11" class="blob-code blob-code-inner js-file-line"><span class="pl-s"><span class="pl-pds"><![CDATA[</span></span></td>
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478 </tr>
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479 <tr>
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480 <td id="L12" class="blob-num js-line-number" data-line-number="12"></td>
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481 <td id="LC12" class="blob-code blob-code-inner js-file-line"><span class="pl-s">mkdir multiqc_WDir &&</span></td>
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482 </tr>
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483 <tr>
|
|
|
484 <td id="L13" class="blob-num js-line-number" data-line-number="13"></td>
|
|
|
485 <td id="LC13" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
|
|
|
486 </tr>
|
|
|
487 <tr>
|
|
|
488 <td id="L14" class="blob-num js-line-number" data-line-number="14"></td>
|
|
|
489 <td id="LC14" class="blob-code blob-code-inner js-file-line"><span class="pl-s">#for $i, $repeat in enumerate( $results )</span></td>
|
|
|
490 </tr>
|
|
|
491 <tr>
|
|
|
492 <td id="L15" class="blob-num js-line-number" data-line-number="15"></td>
|
|
|
493 <td id="LC15" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> mkdir multiqc_WDir/${repeat.software}_${i} &&</span></td>
|
|
|
494 </tr>
|
|
|
495 <tr>
|
|
|
496 <td id="L16" class="blob-num js-line-number" data-line-number="16"></td>
|
|
|
497 <td id="LC16" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
|
|
|
498 </tr>
|
|
|
499 <tr>
|
|
|
500 <td id="L17" class="blob-num js-line-number" data-line-number="17"></td>
|
|
|
501 <td id="LC17" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #if str($repeat.software) == "fastqc":</span></td>
|
|
|
502 </tr>
|
|
|
503 <tr>
|
|
|
504 <td id="L18" class="blob-num js-line-number" data-line-number="18"></td>
|
|
|
505 <td id="LC18" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ## Searches for files named "fastqc_data.txt"</span></td>
|
|
|
506 </tr>
|
|
|
507 <tr>
|
|
|
508 <td id="L19" class="blob-num js-line-number" data-line-number="19"></td>
|
|
|
509 <td id="LC19" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #for $k, $file in enumerate($repeat.input_file):</span></td>
|
|
|
510 </tr>
|
|
|
511 <tr>
|
|
|
512 <td id="L20" class="blob-num js-line-number" data-line-number="20"></td>
|
|
|
513 <td id="LC20" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> mkdir multiqc_WDir/${repeat.software}_${i}/file_${k} &&</span></td>
|
|
|
514 </tr>
|
|
|
515 <tr>
|
|
|
516 <td id="L21" class="blob-num js-line-number" data-line-number="21"></td>
|
|
|
517 <td id="LC21" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '${file}' multiqc_WDir/fastqc_${i}/file_${k}/fastqc_data.txt &&</span></td>
|
|
|
518 </tr>
|
|
|
519 <tr>
|
|
|
520 <td id="L22" class="blob-num js-line-number" data-line-number="22"></td>
|
|
|
521 <td id="LC22" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td>
|
|
|
522 </tr>
|
|
|
523 <tr>
|
|
|
524 <td id="L23" class="blob-num js-line-number" data-line-number="23"></td>
|
|
|
525 <td id="LC23" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == "tophat":</span></td>
|
|
|
526 </tr>
|
|
|
527 <tr>
|
|
|
528 <td id="L24" class="blob-num js-line-number" data-line-number="24"></td>
|
|
|
529 <td id="LC24" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ## Searches for files ending in "align_summary.txt"</span></td>
|
|
|
530 </tr>
|
|
|
531 <tr>
|
|
|
532 <td id="L25" class="blob-num js-line-number" data-line-number="25"></td>
|
|
|
533 <td id="LC25" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #for $file in $repeat.input_file:</span></td>
|
|
|
534 </tr>
|
|
|
535 <tr>
|
|
|
536 <td id="L26" class="blob-num js-line-number" data-line-number="26"></td>
|
|
|
537 <td id="LC26" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}align_summary.txt' &&</span></td>
|
|
|
538 </tr>
|
|
|
539 <tr>
|
|
|
540 <td id="L27" class="blob-num js-line-number" data-line-number="27"></td>
|
|
|
541 <td id="LC27" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td>
|
|
|
542 </tr>
|
|
|
543 <tr>
|
|
|
544 <td id="L28" class="blob-num js-line-number" data-line-number="28"></td>
|
|
|
545 <td id="LC28" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == "bowtie2":</span></td>
|
|
|
546 </tr>
|
|
|
547 <tr>
|
|
|
548 <td id="L29" class="blob-num js-line-number" data-line-number="29"></td>
|
|
|
549 <td id="LC29" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ## Searches for files containing 'reads; of these;'</span></td>
|
|
|
550 </tr>
|
|
|
551 <tr>
|
|
|
552 <td id="L30" class="blob-num js-line-number" data-line-number="30"></td>
|
|
|
553 <td id="LC30" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #for $file in $repeat.input_file:</span></td>
|
|
|
554 </tr>
|
|
|
555 <tr>
|
|
|
556 <td id="L31" class="blob-num js-line-number" data-line-number="31"></td>
|
|
|
557 <td id="LC31" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt' &&</span></td>
|
|
|
558 </tr>
|
|
|
559 <tr>
|
|
|
560 <td id="L32" class="blob-num js-line-number" data-line-number="32"></td>
|
|
|
561 <td id="LC32" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td>
|
|
|
562 </tr>
|
|
|
563 <tr>
|
|
|
564 <td id="L33" class="blob-num js-line-number" data-line-number="33"></td>
|
|
|
565 <td id="LC33" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == "cutadapt":</span></td>
|
|
|
566 </tr>
|
|
|
567 <tr>
|
|
|
568 <td id="L34" class="blob-num js-line-number" data-line-number="34"></td>
|
|
|
569 <td id="LC34" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ## Searches for files containing 'This is cutadapt'</span></td>
|
|
|
570 </tr>
|
|
|
571 <tr>
|
|
|
572 <td id="L35" class="blob-num js-line-number" data-line-number="35"></td>
|
|
|
573 <td id="LC35" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #for $file in $repeat.input_file:</span></td>
|
|
|
574 </tr>
|
|
|
575 <tr>
|
|
|
576 <td id="L36" class="blob-num js-line-number" data-line-number="36"></td>
|
|
|
577 <td id="LC36" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> cat '${file}' > 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt' &&</span></td>
|
|
|
578 </tr>
|
|
|
579 <tr>
|
|
|
580 <td id="L37" class="blob-num js-line-number" data-line-number="37"></td>
|
|
|
581 <td id="LC37" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ## replace header for old cutadapt release</span></td>
|
|
|
582 </tr>
|
|
|
583 <tr>
|
|
|
584 <td id="L38" class="blob-num js-line-number" data-line-number="38"></td>
|
|
|
585 <td id="LC38" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> sed -i .old 's/You are running/This is/' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt' &&</span></td>
|
|
|
586 </tr>
|
|
|
587 <tr>
|
|
|
588 <td id="L39" class="blob-num js-line-number" data-line-number="39"></td>
|
|
|
589 <td id="LC39" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td>
|
|
|
590 </tr>
|
|
|
591 <tr>
|
|
|
592 <td id="L40" class="blob-num js-line-number" data-line-number="40"></td>
|
|
|
593 <td id="LC40" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == "featurecounts":</span></td>
|
|
|
594 </tr>
|
|
|
595 <tr>
|
|
|
596 <td id="L41" class="blob-num js-line-number" data-line-number="41"></td>
|
|
|
597 <td id="LC41" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ## Checks for files ending in '.summary'</span></td>
|
|
|
598 </tr>
|
|
|
599 <tr>
|
|
|
600 <td id="L42" class="blob-num js-line-number" data-line-number="42"></td>
|
|
|
601 <td id="LC42" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #for $file in $repeat.input_file</span></td>
|
|
|
602 </tr>
|
|
|
603 <tr>
|
|
|
604 <td id="L43" class="blob-num js-line-number" data-line-number="43"></td>
|
|
|
605 <td id="LC43" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #if $file.metadata.column_names and $file.metadata.column_names.find(',') != -1</span></td>
|
|
|
606 </tr>
|
|
|
607 <tr>
|
|
|
608 <td id="L44" class="blob-num js-line-number" data-line-number="44"></td>
|
|
|
609 <td id="LC44" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> echo '$file.metadata.column_names.replace(',','\t').replace('__ob__u','').replace('u__sq__','').replace('__sq__','').replace('__cb__','')' >> 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary' &&</span></td>
|
|
|
610 </tr>
|
|
|
611 <tr>
|
|
|
612 <td id="L45" class="blob-num js-line-number" data-line-number="45"></td>
|
|
|
613 <td id="LC45" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> cat '$file' >> 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary' &&</span></td>
|
|
|
614 </tr>
|
|
|
615 <tr>
|
|
|
616 <td id="L46" class="blob-num js-line-number" data-line-number="46"></td>
|
|
|
617 <td id="LC46" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else</span></td>
|
|
|
618 </tr>
|
|
|
619 <tr>
|
|
|
620 <td id="L47" class="blob-num js-line-number" data-line-number="47"></td>
|
|
|
621 <td id="LC47" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '$file' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary' &&</span></td>
|
|
|
622 </tr>
|
|
|
623 <tr>
|
|
|
624 <td id="L48" class="blob-num js-line-number" data-line-number="48"></td>
|
|
|
625 <td id="LC48" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end if</span></td>
|
|
|
626 </tr>
|
|
|
627 <tr>
|
|
|
628 <td id="L49" class="blob-num js-line-number" data-line-number="49"></td>
|
|
|
629 <td id="LC49" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td>
|
|
|
630 </tr>
|
|
|
631 <tr>
|
|
|
632 <td id="L50" class="blob-num js-line-number" data-line-number="50"></td>
|
|
|
633 <td id="LC50" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == "bismark":</span></td>
|
|
|
634 </tr>
|
|
|
635 <tr>
|
|
|
636 <td id="L51" class="blob-num js-line-number" data-line-number="51"></td>
|
|
|
637 <td id="LC51" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ## Checks for files ending in _SE_report.txt</span></td>
|
|
|
638 </tr>
|
|
|
639 <tr>
|
|
|
640 <td id="L52" class="blob-num js-line-number" data-line-number="52"></td>
|
|
|
641 <td id="LC52" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #for $file in $repeat.input_file</span></td>
|
|
|
642 </tr>
|
|
|
643 <tr>
|
|
|
644 <td id="L53" class="blob-num js-line-number" data-line-number="53"></td>
|
|
|
645 <td id="LC53" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s ${file} 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}_SE_report.txt' &&</span></td>
|
|
|
646 </tr>
|
|
|
647 <tr>
|
|
|
648 <td id="L54" class="blob-num js-line-number" data-line-number="54"></td>
|
|
|
649 <td id="LC54" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td>
|
|
|
650 </tr>
|
|
|
651 <tr>
|
|
|
652 <td id="L55" class="blob-num js-line-number" data-line-number="55"></td>
|
|
|
653 <td id="LC55" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == "samtools":</span></td>
|
|
|
654 </tr>
|
|
|
655 <tr>
|
|
|
656 <td id="L56" class="blob-num js-line-number" data-line-number="56"></td>
|
|
|
657 <td id="LC56" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ## Checks for files containing 'This file was produced by samtools stats'</span></td>
|
|
|
658 </tr>
|
|
|
659 <tr>
|
|
|
660 <td id="L57" class="blob-num js-line-number" data-line-number="57"></td>
|
|
|
661 <td id="LC57" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #for $file in $repeat.input_file</span></td>
|
|
|
662 </tr>
|
|
|
663 <tr>
|
|
|
664 <td id="L58" class="blob-num js-line-number" data-line-number="58"></td>
|
|
|
665 <td id="LC58" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s ${file} 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' &&</span></td>
|
|
|
666 </tr>
|
|
|
667 <tr>
|
|
|
668 <td id="L59" class="blob-num js-line-number" data-line-number="59"></td>
|
|
|
669 <td id="LC59" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td>
|
|
|
670 </tr>
|
|
|
671 <tr>
|
|
|
672 <td id="L60" class="blob-num js-line-number" data-line-number="60"></td>
|
|
|
673 <td id="LC60" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == "picard":</span></td>
|
|
|
674 </tr>
|
|
|
675 <tr>
|
|
|
676 <td id="L61" class="blob-num js-line-number" data-line-number="61"></td>
|
|
|
677 <td id="LC61" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #for $file in $repeat.input_file</span></td>
|
|
|
678 </tr>
|
|
|
679 <tr>
|
|
|
680 <td id="L62" class="blob-num js-line-number" data-line-number="62"></td>
|
|
|
681 <td id="LC62" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' &&</span></td>
|
|
|
682 </tr>
|
|
|
683 <tr>
|
|
|
684 <td id="L63" class="blob-num js-line-number" data-line-number="63"></td>
|
|
|
685 <td id="LC63" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td>
|
|
|
686 </tr>
|
|
|
687 <tr>
|
|
|
688 <td id="L64" class="blob-num js-line-number" data-line-number="64"></td>
|
|
|
689 <td id="LC64" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == "samtools_idxstats":</span></td>
|
|
|
690 </tr>
|
|
|
691 <tr>
|
|
|
692 <td id="L65" class="blob-num js-line-number" data-line-number="65"></td>
|
|
|
693 <td id="LC65" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ## Checks for files containing "idxstats" in the name</span></td>
|
|
|
694 </tr>
|
|
|
695 <tr>
|
|
|
696 <td id="L66" class="blob-num js-line-number" data-line-number="66"></td>
|
|
|
697 <td id="LC66" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #for $file in $repeat.input_file</span></td>
|
|
|
698 </tr>
|
|
|
699 <tr>
|
|
|
700 <td id="L67" class="blob-num js-line-number" data-line-number="67"></td>
|
|
|
701 <td id="LC67" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}_idxstats.txt' &&</span></td>
|
|
|
702 </tr>
|
|
|
703 <tr>
|
|
|
704 <td id="L68" class="blob-num js-line-number" data-line-number="68"></td>
|
|
|
705 <td id="LC68" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td>
|
|
|
706 </tr>
|
|
|
707 <tr>
|
|
|
708 <td id="L69" class="blob-num js-line-number" data-line-number="69"></td>
|
|
|
709 <td id="LC69" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == "htseq":</span></td>
|
|
|
710 </tr>
|
|
|
711 <tr>
|
|
|
712 <td id="L70" class="blob-num js-line-number" data-line-number="70"></td>
|
|
|
713 <td id="LC70" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ## Checks for files containing "__too_low_aQual"</span></td>
|
|
|
714 </tr>
|
|
|
715 <tr>
|
|
|
716 <td id="L71" class="blob-num js-line-number" data-line-number="71"></td>
|
|
|
717 <td id="LC71" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #for $file in $repeat.input_file</span></td>
|
|
|
718 </tr>
|
|
|
719 <tr>
|
|
|
720 <td id="L72" class="blob-num js-line-number" data-line-number="72"></td>
|
|
|
721 <td id="LC72" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' &&</span></td>
|
|
|
722 </tr>
|
|
|
723 <tr>
|
|
|
724 <td id="L73" class="blob-num js-line-number" data-line-number="73"></td>
|
|
|
725 <td id="LC73" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td>
|
|
|
726 </tr>
|
|
|
727 <tr>
|
|
|
728 <td id="L74" class="blob-num js-line-number" data-line-number="74"></td>
|
|
|
729 <td id="LC74" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == "rnastar_log":</span></td>
|
|
|
730 </tr>
|
|
|
731 <tr>
|
|
|
732 <td id="L75" class="blob-num js-line-number" data-line-number="75"></td>
|
|
|
733 <td id="LC75" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ## Checks for files named Log.final.out</span></td>
|
|
|
734 </tr>
|
|
|
735 <tr>
|
|
|
736 <td id="L76" class="blob-num js-line-number" data-line-number="76"></td>
|
|
|
737 <td id="LC76" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #for $k, $file in enumerate($repeat.input_file):</span></td>
|
|
|
738 </tr>
|
|
|
739 <tr>
|
|
|
740 <td id="L77" class="blob-num js-line-number" data-line-number="77"></td>
|
|
|
741 <td id="LC77" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> mkdir 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' &&</span></td>
|
|
|
742 </tr>
|
|
|
743 <tr>
|
|
|
744 <td id="L78" class="blob-num js-line-number" data-line-number="78"></td>
|
|
|
745 <td id="LC78" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}/Log.final.out' &&</span></td>
|
|
|
746 </tr>
|
|
|
747 <tr>
|
|
|
748 <td id="L79" class="blob-num js-line-number" data-line-number="79"></td>
|
|
|
749 <td id="LC79" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td>
|
|
|
750 </tr>
|
|
|
751 <tr>
|
|
|
752 <td id="L80" class="blob-num js-line-number" data-line-number="80"></td>
|
|
|
753 <td id="LC80" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #else if str($repeat.software) == "rnastar_counts":</span></td>
|
|
|
754 </tr>
|
|
|
755 <tr>
|
|
|
756 <td id="L81" class="blob-num js-line-number" data-line-number="81"></td>
|
|
|
757 <td id="LC81" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ## Checks for files named ReadsPerGene.out.tab</span></td>
|
|
|
758 </tr>
|
|
|
759 <tr>
|
|
|
760 <td id="L82" class="blob-num js-line-number" data-line-number="82"></td>
|
|
|
761 <td id="LC82" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #for $k, $file in enumerate($repeat.input_file):</span></td>
|
|
|
762 </tr>
|
|
|
763 <tr>
|
|
|
764 <td id="L83" class="blob-num js-line-number" data-line-number="83"></td>
|
|
|
765 <td id="LC83" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> mkdir 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' &&</span></td>
|
|
|
766 </tr>
|
|
|
767 <tr>
|
|
|
768 <td id="L84" class="blob-num js-line-number" data-line-number="84"></td>
|
|
|
769 <td id="LC84" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}/ReadsPerGene.out.tab' &&</span></td>
|
|
|
770 </tr>
|
|
|
771 <tr>
|
|
|
772 <td id="L85" class="blob-num js-line-number" data-line-number="85"></td>
|
|
|
773 <td id="LC85" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end for</span></td>
|
|
|
774 </tr>
|
|
|
775 <tr>
|
|
|
776 <td id="L86" class="blob-num js-line-number" data-line-number="86"></td>
|
|
|
777 <td id="LC86" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> #end if</span></td>
|
|
|
778 </tr>
|
|
|
779 <tr>
|
|
|
780 <td id="L87" class="blob-num js-line-number" data-line-number="87"></td>
|
|
|
781 <td id="LC87" class="blob-code blob-code-inner js-file-line"><span class="pl-s">#end for</span></td>
|
|
|
782 </tr>
|
|
|
783 <tr>
|
|
|
784 <td id="L88" class="blob-num js-line-number" data-line-number="88"></td>
|
|
|
785 <td id="LC88" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
|
|
|
786 </tr>
|
|
|
787 <tr>
|
|
|
788 <td id="L89" class="blob-num js-line-number" data-line-number="89"></td>
|
|
|
789 <td id="LC89" class="blob-code blob-code-inner js-file-line"><span class="pl-s">multiqc multiqc_WDir</span></td>
|
|
|
790 </tr>
|
|
|
791 <tr>
|
|
|
792 <td id="L90" class="blob-num js-line-number" data-line-number="90"></td>
|
|
|
793 <td id="LC90" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> <span class="pl-pds">]]></span></span></<span class="pl-ent">command</span>></td>
|
|
|
794 </tr>
|
|
|
795 <tr>
|
|
|
796 <td id="L91" class="blob-num js-line-number" data-line-number="91"></td>
|
|
|
797 <td id="LC91" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">inputs</span>></td>
|
|
|
798 </tr>
|
|
|
799 <tr>
|
|
|
800 <td id="L92" class="blob-num js-line-number" data-line-number="92"></td>
|
|
|
801 <td id="LC92" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span> <span class="pl-e">title</span>=<span class="pl-s"><span class="pl-pds">"</span>Results<span class="pl-pds">"</span></span> <span class="pl-e">min</span>=<span class="pl-s"><span class="pl-pds">"</span>1<span class="pl-pds">"</span></span>></td>
|
|
|
802 </tr>
|
|
|
803 <tr>
|
|
|
804 <td id="L93" class="blob-num js-line-number" data-line-number="93"></td>
|
|
|
805 <td id="LC93" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>select<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Software name<span class="pl-pds">"</span></span> <span class="pl-e">help</span>=<span class="pl-s"><span class="pl-pds">"</span>Which tool was used generate logs?<span class="pl-pds">"</span></span>></td>
|
|
|
806 </tr>
|
|
|
807 <tr>
|
|
|
808 <td id="L94" class="blob-num js-line-number" data-line-number="94"></td>
|
|
|
809 <td id="LC94" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>fastqc<span class="pl-pds">"</span></span>>FastQC</<span class="pl-ent">option</span>></td>
|
|
|
810 </tr>
|
|
|
811 <tr>
|
|
|
812 <td id="L95" class="blob-num js-line-number" data-line-number="95"></td>
|
|
|
813 <td id="LC95" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>cutadapt<span class="pl-pds">"</span></span>>Cutadapt/Trim Galore!</<span class="pl-ent">option</span>></td>
|
|
|
814 </tr>
|
|
|
815 <tr>
|
|
|
816 <td id="L96" class="blob-num js-line-number" data-line-number="96"></td>
|
|
|
817 <td id="LC96" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>tophat<span class="pl-pds">"</span></span>>Tophat2</<span class="pl-ent">option</span>></td>
|
|
|
818 </tr>
|
|
|
819 <tr>
|
|
|
820 <td id="L97" class="blob-num js-line-number" data-line-number="97"></td>
|
|
|
821 <td id="LC97" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>featurecounts<span class="pl-pds">"</span></span>>FeatureCounts (Summary file)</<span class="pl-ent">option</span>></td>
|
|
|
822 </tr>
|
|
|
823 <tr>
|
|
|
824 <td id="L98" class="blob-num js-line-number" data-line-number="98"></td>
|
|
|
825 <td id="LC98" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>samtools<span class="pl-pds">"</span></span>>Samtools (Stats, Flagstat)</<span class="pl-ent">option</span>></td>
|
|
|
826 </tr>
|
|
|
827 <tr>
|
|
|
828 <td id="L99" class="blob-num js-line-number" data-line-number="99"></td>
|
|
|
829 <td id="LC99" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>samtools_idxstats<span class="pl-pds">"</span></span>>Samtools (Idxstats)</<span class="pl-ent">option</span>></td>
|
|
|
830 </tr>
|
|
|
831 <tr>
|
|
|
832 <td id="L100" class="blob-num js-line-number" data-line-number="100"></td>
|
|
|
833 <td id="LC100" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>picard<span class="pl-pds">"</span></span>>Picard</<span class="pl-ent">option</span>></td>
|
|
|
834 </tr>
|
|
|
835 <tr>
|
|
|
836 <td id="L101" class="blob-num js-line-number" data-line-number="101"></td>
|
|
|
837 <td id="LC101" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>bismark<span class="pl-pds">"</span></span>>Bismark</<span class="pl-ent">option</span>></td>
|
|
|
838 </tr>
|
|
|
839 <tr>
|
|
|
840 <td id="L102" class="blob-num js-line-number" data-line-number="102"></td>
|
|
|
841 <td id="LC102" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>bowtie2<span class="pl-pds">"</span></span>>Bowtie2</<span class="pl-ent">option</span>></td>
|
|
|
842 </tr>
|
|
|
843 <tr>
|
|
|
844 <td id="L103" class="blob-num js-line-number" data-line-number="103"></td>
|
|
|
845 <td id="LC103" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>htseq<span class="pl-pds">"</span></span>>HTSeq-Count</<span class="pl-ent">option</span>></td>
|
|
|
846 </tr>
|
|
|
847 <tr>
|
|
|
848 <td id="L104" class="blob-num js-line-number" data-line-number="104"></td>
|
|
|
849 <td id="LC104" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>rnastar_log<span class="pl-pds">"</span></span>>RNA STAR (log)</<span class="pl-ent">option</span>></td>
|
|
|
850 </tr>
|
|
|
851 <tr>
|
|
|
852 <td id="L105" class="blob-num js-line-number" data-line-number="105"></td>
|
|
|
853 <td id="LC105" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>rnastar_counts<span class="pl-pds">"</span></span>>RNA STAR (reads per gene)</<span class="pl-ent">option</span>></td>
|
|
|
854 </tr>
|
|
|
855 <tr>
|
|
|
856 <td id="L106" class="blob-num js-line-number" data-line-number="106"></td>
|
|
|
857 <td id="LC106" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">param</span>></td>
|
|
|
858 </tr>
|
|
|
859 <tr>
|
|
|
860 <td id="L107" class="blob-num js-line-number" data-line-number="107"></td>
|
|
|
861 <td id="LC107" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>data<span class="pl-pds">"</span></span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">"</span>txt, tabular<span class="pl-pds">"</span></span> <span class="pl-e">multiple</span>=<span class="pl-s"><span class="pl-pds">"</span>true<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Result file<span class="pl-pds">"</span></span> <span class="pl-e">help</span>=<span class="pl-s"><span class="pl-pds">"</span>Select input datasets<span class="pl-pds">"</span></span>/></td>
|
|
|
862 </tr>
|
|
|
863 <tr>
|
|
|
864 <td id="L108" class="blob-num js-line-number" data-line-number="108"></td>
|
|
|
865 <td id="LC108" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">repeat</span>></td>
|
|
|
866 </tr>
|
|
|
867 <tr>
|
|
|
868 <td id="L109" class="blob-num js-line-number" data-line-number="109"></td>
|
|
|
869 <td id="LC109" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>saveLog<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>boolean<span class="pl-pds">"</span></span> <span class="pl-e">truevalue</span>=<span class="pl-s"><span class="pl-pds">"</span>true<span class="pl-pds">"</span></span> <span class="pl-e">falsevalue</span>=<span class="pl-s"><span class="pl-pds">"</span>false<span class="pl-pds">"</span></span> <span class="pl-e">checked</span>=<span class="pl-s"><span class="pl-pds">"</span>false<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Save log file<span class="pl-pds">"</span></span> <span class="pl-e">help</span>=<span class="pl-s"><span class="pl-pds">"</span>Save the multiQC log file to the history. This is mostly useful for debugging purposes.<span class="pl-pds">"</span></span>/></td>
|
|
|
870 </tr>
|
|
|
871 <tr>
|
|
|
872 <td id="L110" class="blob-num js-line-number" data-line-number="110"></td>
|
|
|
873 <td id="LC110" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">inputs</span>></td>
|
|
|
874 </tr>
|
|
|
875 <tr>
|
|
|
876 <td id="L111" class="blob-num js-line-number" data-line-number="111"></td>
|
|
|
877 <td id="LC111" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">outputs</span>></td>
|
|
|
878 </tr>
|
|
|
879 <tr>
|
|
|
880 <td id="L112" class="blob-num js-line-number" data-line-number="112"></td>
|
|
|
881 <td id="LC112" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">data</span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">"</span>html<span class="pl-pds">"</span></span> <span class="pl-e">from_work_dir</span>=<span class="pl-s"><span class="pl-pds">"</span>multiqc_report.html<span class="pl-pds">"</span></span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>${tool.name} on ${on_string}: Webpage<span class="pl-pds">"</span></span> /></td>
|
|
|
882 </tr>
|
|
|
883 <tr>
|
|
|
884 <td id="L113" class="blob-num js-line-number" data-line-number="113"></td>
|
|
|
885 <td id="LC113" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">data</span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">"</span>txt<span class="pl-pds">"</span></span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>text_file<span class="pl-pds">"</span></span> <span class="pl-e">from_work_dir</span>=<span class="pl-s"><span class="pl-pds">"</span>multiqc_data/multiqc.log<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>${tool.name} on ${on_string}: Log<span class="pl-pds">"</span></span>></td>
|
|
|
886 </tr>
|
|
|
887 <tr>
|
|
|
888 <td id="L114" class="blob-num js-line-number" data-line-number="114"></td>
|
|
|
889 <td id="LC114" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">filter</span>>saveLog</<span class="pl-ent">filter</span>></td>
|
|
|
890 </tr>
|
|
|
891 <tr>
|
|
|
892 <td id="L115" class="blob-num js-line-number" data-line-number="115"></td>
|
|
|
893 <td id="LC115" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">data</span>></td>
|
|
|
894 </tr>
|
|
|
895 <tr>
|
|
|
896 <td id="L116" class="blob-num js-line-number" data-line-number="116"></td>
|
|
|
897 <td id="LC116" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">outputs</span>></td>
|
|
|
898 </tr>
|
|
|
899 <tr>
|
|
|
900 <td id="L117" class="blob-num js-line-number" data-line-number="117"></td>
|
|
|
901 <td id="LC117" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">tests</span>></td>
|
|
|
902 </tr>
|
|
|
903 <tr>
|
|
|
904 <td id="L118" class="blob-num js-line-number" data-line-number="118"></td>
|
|
|
905 <td id="LC118" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">test</span>></td>
|
|
|
906 </tr>
|
|
|
907 <tr>
|
|
|
908 <td id="L119" class="blob-num js-line-number" data-line-number="119"></td>
|
|
|
909 <td id="LC119" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td>
|
|
|
910 </tr>
|
|
|
911 <tr>
|
|
|
912 <td id="L120" class="blob-num js-line-number" data-line-number="120"></td>
|
|
|
913 <td id="LC120" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>fastqc<span class="pl-pds">"</span></span> /></td>
|
|
|
914 </tr>
|
|
|
915 <tr>
|
|
|
916 <td id="L121" class="blob-num js-line-number" data-line-number="121"></td>
|
|
|
917 <td id="LC121" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>fastqc_data.txt<span class="pl-pds">"</span></span> /></td>
|
|
|
918 </tr>
|
|
|
919 <tr>
|
|
|
920 <td id="L122" class="blob-num js-line-number" data-line-number="122"></td>
|
|
|
921 <td id="LC122" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">repeat</span>></td>
|
|
|
922 </tr>
|
|
|
923 <tr>
|
|
|
924 <td id="L123" class="blob-num js-line-number" data-line-number="123"></td>
|
|
|
925 <td id="LC123" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>saveLog<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>True<span class="pl-pds">"</span></span>/></td>
|
|
|
926 </tr>
|
|
|
927 <tr>
|
|
|
928 <td id="L124" class="blob-num js-line-number" data-line-number="124"></td>
|
|
|
929 <td id="LC124" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_fastqc.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td>
|
|
|
930 </tr>
|
|
|
931 <tr>
|
|
|
932 <td id="L125" class="blob-num js-line-number" data-line-number="125"></td>
|
|
|
933 <td id="LC125" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>text_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>log_fastqc.txt<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td>
|
|
|
934 </tr>
|
|
|
935 <tr>
|
|
|
936 <td id="L126" class="blob-num js-line-number" data-line-number="126"></td>
|
|
|
937 <td id="LC126" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">test</span>></td>
|
|
|
938 </tr>
|
|
|
939 <tr>
|
|
|
940 <td id="L127" class="blob-num js-line-number" data-line-number="127"></td>
|
|
|
941 <td id="LC127" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">test</span>></td>
|
|
|
942 </tr>
|
|
|
943 <tr>
|
|
|
944 <td id="L128" class="blob-num js-line-number" data-line-number="128"></td>
|
|
|
945 <td id="LC128" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td>
|
|
|
946 </tr>
|
|
|
947 <tr>
|
|
|
948 <td id="L129" class="blob-num js-line-number" data-line-number="129"></td>
|
|
|
949 <td id="LC129" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>fastqc<span class="pl-pds">"</span></span> /></td>
|
|
|
950 </tr>
|
|
|
951 <tr>
|
|
|
952 <td id="L130" class="blob-num js-line-number" data-line-number="130"></td>
|
|
|
953 <td id="LC130" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>fastqc_data.txt,fastqc_data_2.txt<span class="pl-pds">"</span></span> /></td>
|
|
|
954 </tr>
|
|
|
955 <tr>
|
|
|
956 <td id="L131" class="blob-num js-line-number" data-line-number="131"></td>
|
|
|
957 <td id="LC131" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">repeat</span>></td>
|
|
|
958 </tr>
|
|
|
959 <tr>
|
|
|
960 <td id="L132" class="blob-num js-line-number" data-line-number="132"></td>
|
|
|
961 <td id="LC132" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_fastqc_2.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td>
|
|
|
962 </tr>
|
|
|
963 <tr>
|
|
|
964 <td id="L133" class="blob-num js-line-number" data-line-number="133"></td>
|
|
|
965 <td id="LC133" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">test</span>></td>
|
|
|
966 </tr>
|
|
|
967 <tr>
|
|
|
968 <td id="L134" class="blob-num js-line-number" data-line-number="134"></td>
|
|
|
969 <td id="LC134" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">test</span>></td>
|
|
|
970 </tr>
|
|
|
971 <tr>
|
|
|
972 <td id="L135" class="blob-num js-line-number" data-line-number="135"></td>
|
|
|
973 <td id="LC135" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td>
|
|
|
974 </tr>
|
|
|
975 <tr>
|
|
|
976 <td id="L136" class="blob-num js-line-number" data-line-number="136"></td>
|
|
|
977 <td id="LC136" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>cutadapt<span class="pl-pds">"</span></span> /></td>
|
|
|
978 </tr>
|
|
|
979 <tr>
|
|
|
980 <td id="L137" class="blob-num js-line-number" data-line-number="137"></td>
|
|
|
981 <td id="LC137" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>cutadapt.txt<span class="pl-pds">"</span></span> /></td>
|
|
|
982 </tr>
|
|
|
983 <tr>
|
|
|
984 <td id="L138" class="blob-num js-line-number" data-line-number="138"></td>
|
|
|
985 <td id="LC138" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">repeat</span>></td>
|
|
|
986 </tr>
|
|
|
987 <tr>
|
|
|
988 <td id="L139" class="blob-num js-line-number" data-line-number="139"></td>
|
|
|
989 <td id="LC139" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_cutadapt.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td>
|
|
|
990 </tr>
|
|
|
991 <tr>
|
|
|
992 <td id="L140" class="blob-num js-line-number" data-line-number="140"></td>
|
|
|
993 <td id="LC140" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">test</span>></td>
|
|
|
994 </tr>
|
|
|
995 <tr>
|
|
|
996 <td id="L141" class="blob-num js-line-number" data-line-number="141"></td>
|
|
|
997 <td id="LC141" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">test</span>></td>
|
|
|
998 </tr>
|
|
|
999 <tr>
|
|
|
1000 <td id="L142" class="blob-num js-line-number" data-line-number="142"></td>
|
|
|
1001 <td id="LC142" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td>
|
|
|
1002 </tr>
|
|
|
1003 <tr>
|
|
|
1004 <td id="L143" class="blob-num js-line-number" data-line-number="143"></td>
|
|
|
1005 <td id="LC143" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>tophat<span class="pl-pds">"</span></span> /></td>
|
|
|
1006 </tr>
|
|
|
1007 <tr>
|
|
|
1008 <td id="L144" class="blob-num js-line-number" data-line-number="144"></td>
|
|
|
1009 <td id="LC144" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>tophat_data.txt<span class="pl-pds">"</span></span> /></td>
|
|
|
1010 </tr>
|
|
|
1011 <tr>
|
|
|
1012 <td id="L145" class="blob-num js-line-number" data-line-number="145"></td>
|
|
|
1013 <td id="LC145" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">repeat</span>></td>
|
|
|
1014 </tr>
|
|
|
1015 <tr>
|
|
|
1016 <td id="L146" class="blob-num js-line-number" data-line-number="146"></td>
|
|
|
1017 <td id="LC146" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_tophat.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td>
|
|
|
1018 </tr>
|
|
|
1019 <tr>
|
|
|
1020 <td id="L147" class="blob-num js-line-number" data-line-number="147"></td>
|
|
|
1021 <td id="LC147" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">test</span>></td>
|
|
|
1022 </tr>
|
|
|
1023 <tr>
|
|
|
1024 <td id="L148" class="blob-num js-line-number" data-line-number="148"></td>
|
|
|
1025 <td id="LC148" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">test</span>></td>
|
|
|
1026 </tr>
|
|
|
1027 <tr>
|
|
|
1028 <td id="L149" class="blob-num js-line-number" data-line-number="149"></td>
|
|
|
1029 <td id="LC149" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td>
|
|
|
1030 </tr>
|
|
|
1031 <tr>
|
|
|
1032 <td id="L150" class="blob-num js-line-number" data-line-number="150"></td>
|
|
|
1033 <td id="LC150" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>bowtie2<span class="pl-pds">"</span></span> /></td>
|
|
|
1034 </tr>
|
|
|
1035 <tr>
|
|
|
1036 <td id="L151" class="blob-num js-line-number" data-line-number="151"></td>
|
|
|
1037 <td id="LC151" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>bowtie2SE1.txt,bowtie2SE2.txt<span class="pl-pds">"</span></span> /></td>
|
|
|
1038 </tr>
|
|
|
1039 <tr>
|
|
|
1040 <td id="L152" class="blob-num js-line-number" data-line-number="152"></td>
|
|
|
1041 <td id="LC152" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">repeat</span>></td>
|
|
|
1042 </tr>
|
|
|
1043 <tr>
|
|
|
1044 <td id="L153" class="blob-num js-line-number" data-line-number="153"></td>
|
|
|
1045 <td id="LC153" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_bowtie2SE.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td>
|
|
|
1046 </tr>
|
|
|
1047 <tr>
|
|
|
1048 <td id="L154" class="blob-num js-line-number" data-line-number="154"></td>
|
|
|
1049 <td id="LC154" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">test</span>></td>
|
|
|
1050 </tr>
|
|
|
1051 <tr>
|
|
|
1052 <td id="L155" class="blob-num js-line-number" data-line-number="155"></td>
|
|
|
1053 <td id="LC155" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">test</span>></td>
|
|
|
1054 </tr>
|
|
|
1055 <tr>
|
|
|
1056 <td id="L156" class="blob-num js-line-number" data-line-number="156"></td>
|
|
|
1057 <td id="LC156" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td>
|
|
|
1058 </tr>
|
|
|
1059 <tr>
|
|
|
1060 <td id="L157" class="blob-num js-line-number" data-line-number="157"></td>
|
|
|
1061 <td id="LC157" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>featurecounts<span class="pl-pds">"</span></span> /></td>
|
|
|
1062 </tr>
|
|
|
1063 <tr>
|
|
|
1064 <td id="L158" class="blob-num js-line-number" data-line-number="158"></td>
|
|
|
1065 <td id="LC158" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>featurecounts_data.txt<span class="pl-pds">"</span></span> /></td>
|
|
|
1066 </tr>
|
|
|
1067 <tr>
|
|
|
1068 <td id="L159" class="blob-num js-line-number" data-line-number="159"></td>
|
|
|
1069 <td id="LC159" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">repeat</span>></td>
|
|
|
1070 </tr>
|
|
|
1071 <tr>
|
|
|
1072 <td id="L160" class="blob-num js-line-number" data-line-number="160"></td>
|
|
|
1073 <td id="LC160" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_featurecounts.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td>
|
|
|
1074 </tr>
|
|
|
1075 <tr>
|
|
|
1076 <td id="L161" class="blob-num js-line-number" data-line-number="161"></td>
|
|
|
1077 <td id="LC161" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">test</span>></td>
|
|
|
1078 </tr>
|
|
|
1079 <tr>
|
|
|
1080 <td id="L162" class="blob-num js-line-number" data-line-number="162"></td>
|
|
|
1081 <td id="LC162" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">test</span>></td>
|
|
|
1082 </tr>
|
|
|
1083 <tr>
|
|
|
1084 <td id="L163" class="blob-num js-line-number" data-line-number="163"></td>
|
|
|
1085 <td id="LC163" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td>
|
|
|
1086 </tr>
|
|
|
1087 <tr>
|
|
|
1088 <td id="L164" class="blob-num js-line-number" data-line-number="164"></td>
|
|
|
1089 <td id="LC164" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>picard<span class="pl-pds">"</span></span> /></td>
|
|
|
1090 </tr>
|
|
|
1091 <tr>
|
|
|
1092 <td id="L165" class="blob-num js-line-number" data-line-number="165"></td>
|
|
|
1093 <td id="LC165" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt,picard_CollectBaseDistributionByCycle.txt,picard_CollectRnaSeqMetrics.txt,picard_CollectAlignmentSummaryMetrics.txt<span class="pl-pds">"</span></span> /></td>
|
|
|
1094 </tr>
|
|
|
1095 <tr>
|
|
|
1096 <td id="L166" class="blob-num js-line-number" data-line-number="166"></td>
|
|
|
1097 <td id="LC166" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">repeat</span>></td>
|
|
|
1098 </tr>
|
|
|
1099 <tr>
|
|
|
1100 <td id="L167" class="blob-num js-line-number" data-line-number="167"></td>
|
|
|
1101 <td id="LC167" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_picard.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>10000<span class="pl-pds">"</span></span>/></td>
|
|
|
1102 </tr>
|
|
|
1103 <tr>
|
|
|
1104 <td id="L168" class="blob-num js-line-number" data-line-number="168"></td>
|
|
|
1105 <td id="LC168" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">test</span>></td>
|
|
|
1106 </tr>
|
|
|
1107 <tr>
|
|
|
1108 <td id="L169" class="blob-num js-line-number" data-line-number="169"></td>
|
|
|
1109 <td id="LC169" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">test</span>></td>
|
|
|
1110 </tr>
|
|
|
1111 <tr>
|
|
|
1112 <td id="L170" class="blob-num js-line-number" data-line-number="170"></td>
|
|
|
1113 <td id="LC170" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td>
|
|
|
1114 </tr>
|
|
|
1115 <tr>
|
|
|
1116 <td id="L171" class="blob-num js-line-number" data-line-number="171"></td>
|
|
|
1117 <td id="LC171" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>htseq<span class="pl-pds">"</span></span> /></td>
|
|
|
1118 </tr>
|
|
|
1119 <tr>
|
|
|
1120 <td id="L172" class="blob-num js-line-number" data-line-number="172"></td>
|
|
|
1121 <td id="LC172" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>htseq_data.txt<span class="pl-pds">"</span></span> /></td>
|
|
|
1122 </tr>
|
|
|
1123 <tr>
|
|
|
1124 <td id="L173" class="blob-num js-line-number" data-line-number="173"></td>
|
|
|
1125 <td id="LC173" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">repeat</span>></td>
|
|
|
1126 </tr>
|
|
|
1127 <tr>
|
|
|
1128 <td id="L174" class="blob-num js-line-number" data-line-number="174"></td>
|
|
|
1129 <td id="LC174" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_htseq.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td>
|
|
|
1130 </tr>
|
|
|
1131 <tr>
|
|
|
1132 <td id="L175" class="blob-num js-line-number" data-line-number="175"></td>
|
|
|
1133 <td id="LC175" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">test</span>></td>
|
|
|
1134 </tr>
|
|
|
1135 <tr>
|
|
|
1136 <td id="L176" class="blob-num js-line-number" data-line-number="176"></td>
|
|
|
1137 <td id="LC176" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">test</span>></td>
|
|
|
1138 </tr>
|
|
|
1139 <tr>
|
|
|
1140 <td id="L177" class="blob-num js-line-number" data-line-number="177"></td>
|
|
|
1141 <td id="LC177" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td>
|
|
|
1142 </tr>
|
|
|
1143 <tr>
|
|
|
1144 <td id="L178" class="blob-num js-line-number" data-line-number="178"></td>
|
|
|
1145 <td id="LC178" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>rnastar_log<span class="pl-pds">"</span></span> /></td>
|
|
|
1146 </tr>
|
|
|
1147 <tr>
|
|
|
1148 <td id="L179" class="blob-num js-line-number" data-line-number="179"></td>
|
|
|
1149 <td id="LC179" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>rnastar_log.txt<span class="pl-pds">"</span></span> /></td>
|
|
|
1150 </tr>
|
|
|
1151 <tr>
|
|
|
1152 <td id="L180" class="blob-num js-line-number" data-line-number="180"></td>
|
|
|
1153 <td id="LC180" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">repeat</span>></td>
|
|
|
1154 </tr>
|
|
|
1155 <tr>
|
|
|
1156 <td id="L181" class="blob-num js-line-number" data-line-number="181"></td>
|
|
|
1157 <td id="LC181" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_rnastar_log.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td>
|
|
|
1158 </tr>
|
|
|
1159 <tr>
|
|
|
1160 <td id="L182" class="blob-num js-line-number" data-line-number="182"></td>
|
|
|
1161 <td id="LC182" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">test</span>></td>
|
|
|
1162 </tr>
|
|
|
1163 <tr>
|
|
|
1164 <td id="L183" class="blob-num js-line-number" data-line-number="183"></td>
|
|
|
1165 <td id="LC183" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">test</span>></td>
|
|
|
1166 </tr>
|
|
|
1167 <tr>
|
|
|
1168 <td id="L184" class="blob-num js-line-number" data-line-number="184"></td>
|
|
|
1169 <td id="LC184" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td>
|
|
|
1170 </tr>
|
|
|
1171 <tr>
|
|
|
1172 <td id="L185" class="blob-num js-line-number" data-line-number="185"></td>
|
|
|
1173 <td id="LC185" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>rnastar_counts<span class="pl-pds">"</span></span> /></td>
|
|
|
1174 </tr>
|
|
|
1175 <tr>
|
|
|
1176 <td id="L186" class="blob-num js-line-number" data-line-number="186"></td>
|
|
|
1177 <td id="LC186" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>rnastar_counts.txt<span class="pl-pds">"</span></span> /></td>
|
|
|
1178 </tr>
|
|
|
1179 <tr>
|
|
|
1180 <td id="L187" class="blob-num js-line-number" data-line-number="187"></td>
|
|
|
1181 <td id="LC187" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">repeat</span>></td>
|
|
|
1182 </tr>
|
|
|
1183 <tr>
|
|
|
1184 <td id="L188" class="blob-num js-line-number" data-line-number="188"></td>
|
|
|
1185 <td id="LC188" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_rnastar_counts.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td>
|
|
|
1186 </tr>
|
|
|
1187 <tr>
|
|
|
1188 <td id="L189" class="blob-num js-line-number" data-line-number="189"></td>
|
|
|
1189 <td id="LC189" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">test</span>></td>
|
|
|
1190 </tr>
|
|
|
1191 <tr>
|
|
|
1192 <td id="L190" class="blob-num js-line-number" data-line-number="190"></td>
|
|
|
1193 <td id="LC190" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">test</span>></td>
|
|
|
1194 </tr>
|
|
|
1195 <tr>
|
|
|
1196 <td id="L191" class="blob-num js-line-number" data-line-number="191"></td>
|
|
|
1197 <td id="LC191" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td>
|
|
|
1198 </tr>
|
|
|
1199 <tr>
|
|
|
1200 <td id="L192" class="blob-num js-line-number" data-line-number="192"></td>
|
|
|
1201 <td id="LC192" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>bismark<span class="pl-pds">"</span></span> /></td>
|
|
|
1202 </tr>
|
|
|
1203 <tr>
|
|
|
1204 <td id="L193" class="blob-num js-line-number" data-line-number="193"></td>
|
|
|
1205 <td id="LC193" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>bismark_data.txt<span class="pl-pds">"</span></span> /></td>
|
|
|
1206 </tr>
|
|
|
1207 <tr>
|
|
|
1208 <td id="L194" class="blob-num js-line-number" data-line-number="194"></td>
|
|
|
1209 <td id="LC194" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">repeat</span>></td>
|
|
|
1210 </tr>
|
|
|
1211 <tr>
|
|
|
1212 <td id="L195" class="blob-num js-line-number" data-line-number="195"></td>
|
|
|
1213 <td id="LC195" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_bismark.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td>
|
|
|
1214 </tr>
|
|
|
1215 <tr>
|
|
|
1216 <td id="L196" class="blob-num js-line-number" data-line-number="196"></td>
|
|
|
1217 <td id="LC196" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">test</span>></td>
|
|
|
1218 </tr>
|
|
|
1219 <tr>
|
|
|
1220 <td id="L197" class="blob-num js-line-number" data-line-number="197"></td>
|
|
|
1221 <td id="LC197" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">test</span>></td>
|
|
|
1222 </tr>
|
|
|
1223 <tr>
|
|
|
1224 <td id="L198" class="blob-num js-line-number" data-line-number="198"></td>
|
|
|
1225 <td id="LC198" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td>
|
|
|
1226 </tr>
|
|
|
1227 <tr>
|
|
|
1228 <td id="L199" class="blob-num js-line-number" data-line-number="199"></td>
|
|
|
1229 <td id="LC199" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>samtools<span class="pl-pds">"</span></span> /></td>
|
|
|
1230 </tr>
|
|
|
1231 <tr>
|
|
|
1232 <td id="L200" class="blob-num js-line-number" data-line-number="200"></td>
|
|
|
1233 <td id="LC200" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>samtools_stats.txt,samtools_flagstat.txt<span class="pl-pds">"</span></span> /></td>
|
|
|
1234 </tr>
|
|
|
1235 <tr>
|
|
|
1236 <td id="L201" class="blob-num js-line-number" data-line-number="201"></td>
|
|
|
1237 <td id="LC201" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">repeat</span>></td>
|
|
|
1238 </tr>
|
|
|
1239 <tr>
|
|
|
1240 <td id="L202" class="blob-num js-line-number" data-line-number="202"></td>
|
|
|
1241 <td id="LC202" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_samtools.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td>
|
|
|
1242 </tr>
|
|
|
1243 <tr>
|
|
|
1244 <td id="L203" class="blob-num js-line-number" data-line-number="203"></td>
|
|
|
1245 <td id="LC203" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">test</span>></td>
|
|
|
1246 </tr>
|
|
|
1247 <tr>
|
|
|
1248 <td id="L204" class="blob-num js-line-number" data-line-number="204"></td>
|
|
|
1249 <td id="LC204" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">test</span>></td>
|
|
|
1250 </tr>
|
|
|
1251 <tr>
|
|
|
1252 <td id="L205" class="blob-num js-line-number" data-line-number="205"></td>
|
|
|
1253 <td id="LC205" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td>
|
|
|
1254 </tr>
|
|
|
1255 <tr>
|
|
|
1256 <td id="L206" class="blob-num js-line-number" data-line-number="206"></td>
|
|
|
1257 <td id="LC206" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>samtools_idxstats<span class="pl-pds">"</span></span> /></td>
|
|
|
1258 </tr>
|
|
|
1259 <tr>
|
|
|
1260 <td id="L207" class="blob-num js-line-number" data-line-number="207"></td>
|
|
|
1261 <td id="LC207" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>samtools_idxstats.txt<span class="pl-pds">"</span></span> /></td>
|
|
|
1262 </tr>
|
|
|
1263 <tr>
|
|
|
1264 <td id="L208" class="blob-num js-line-number" data-line-number="208"></td>
|
|
|
1265 <td id="LC208" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">repeat</span>></td>
|
|
|
1266 </tr>
|
|
|
1267 <tr>
|
|
|
1268 <td id="L209" class="blob-num js-line-number" data-line-number="209"></td>
|
|
|
1269 <td id="LC209" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_samtools_idxstats.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>1000<span class="pl-pds">"</span></span>/></td>
|
|
|
1270 </tr>
|
|
|
1271 <tr>
|
|
|
1272 <td id="L210" class="blob-num js-line-number" data-line-number="210"></td>
|
|
|
1273 <td id="LC210" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">test</span>></td>
|
|
|
1274 </tr>
|
|
|
1275 <tr>
|
|
|
1276 <td id="L211" class="blob-num js-line-number" data-line-number="211"></td>
|
|
|
1277 <td id="LC211" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">test</span>></td>
|
|
|
1278 </tr>
|
|
|
1279 <tr>
|
|
|
1280 <td id="L212" class="blob-num js-line-number" data-line-number="212"></td>
|
|
|
1281 <td id="LC212" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td>
|
|
|
1282 </tr>
|
|
|
1283 <tr>
|
|
|
1284 <td id="L213" class="blob-num js-line-number" data-line-number="213"></td>
|
|
|
1285 <td id="LC213" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>fastqc<span class="pl-pds">"</span></span> /></td>
|
|
|
1286 </tr>
|
|
|
1287 <tr>
|
|
|
1288 <td id="L214" class="blob-num js-line-number" data-line-number="214"></td>
|
|
|
1289 <td id="LC214" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>fastqc_data.txt,fastqc_data_2.txt<span class="pl-pds">"</span></span> /></td>
|
|
|
1290 </tr>
|
|
|
1291 <tr>
|
|
|
1292 <td id="L215" class="blob-num js-line-number" data-line-number="215"></td>
|
|
|
1293 <td id="LC215" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">repeat</span>></td>
|
|
|
1294 </tr>
|
|
|
1295 <tr>
|
|
|
1296 <td id="L216" class="blob-num js-line-number" data-line-number="216"></td>
|
|
|
1297 <td id="LC216" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td>
|
|
|
1298 </tr>
|
|
|
1299 <tr>
|
|
|
1300 <td id="L217" class="blob-num js-line-number" data-line-number="217"></td>
|
|
|
1301 <td id="LC217" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>cutadapt<span class="pl-pds">"</span></span> /></td>
|
|
|
1302 </tr>
|
|
|
1303 <tr>
|
|
|
1304 <td id="L218" class="blob-num js-line-number" data-line-number="218"></td>
|
|
|
1305 <td id="LC218" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>cutadapt.txt<span class="pl-pds">"</span></span> /></td>
|
|
|
1306 </tr>
|
|
|
1307 <tr>
|
|
|
1308 <td id="L219" class="blob-num js-line-number" data-line-number="219"></td>
|
|
|
1309 <td id="LC219" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">repeat</span>></td>
|
|
|
1310 </tr>
|
|
|
1311 <tr>
|
|
|
1312 <td id="L220" class="blob-num js-line-number" data-line-number="220"></td>
|
|
|
1313 <td id="LC220" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td>
|
|
|
1314 </tr>
|
|
|
1315 <tr>
|
|
|
1316 <td id="L221" class="blob-num js-line-number" data-line-number="221"></td>
|
|
|
1317 <td id="LC221" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>tophat<span class="pl-pds">"</span></span> /></td>
|
|
|
1318 </tr>
|
|
|
1319 <tr>
|
|
|
1320 <td id="L222" class="blob-num js-line-number" data-line-number="222"></td>
|
|
|
1321 <td id="LC222" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>tophat_data.txt<span class="pl-pds">"</span></span> /></td>
|
|
|
1322 </tr>
|
|
|
1323 <tr>
|
|
|
1324 <td id="L223" class="blob-num js-line-number" data-line-number="223"></td>
|
|
|
1325 <td id="LC223" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">repeat</span>></td>
|
|
|
1326 </tr>
|
|
|
1327 <tr>
|
|
|
1328 <td id="L224" class="blob-num js-line-number" data-line-number="224"></td>
|
|
|
1329 <td id="LC224" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td>
|
|
|
1330 </tr>
|
|
|
1331 <tr>
|
|
|
1332 <td id="L225" class="blob-num js-line-number" data-line-number="225"></td>
|
|
|
1333 <td id="LC225" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>featurecounts<span class="pl-pds">"</span></span> /></td>
|
|
|
1334 </tr>
|
|
|
1335 <tr>
|
|
|
1336 <td id="L226" class="blob-num js-line-number" data-line-number="226"></td>
|
|
|
1337 <td id="LC226" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>featurecounts_data.txt<span class="pl-pds">"</span></span> /></td>
|
|
|
1338 </tr>
|
|
|
1339 <tr>
|
|
|
1340 <td id="L227" class="blob-num js-line-number" data-line-number="227"></td>
|
|
|
1341 <td id="LC227" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">repeat</span>></td>
|
|
|
1342 </tr>
|
|
|
1343 <tr>
|
|
|
1344 <td id="L228" class="blob-num js-line-number" data-line-number="228"></td>
|
|
|
1345 <td id="LC228" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td>
|
|
|
1346 </tr>
|
|
|
1347 <tr>
|
|
|
1348 <td id="L229" class="blob-num js-line-number" data-line-number="229"></td>
|
|
|
1349 <td id="LC229" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>picard<span class="pl-pds">"</span></span> /></td>
|
|
|
1350 </tr>
|
|
|
1351 <tr>
|
|
|
1352 <td id="L230" class="blob-num js-line-number" data-line-number="230"></td>
|
|
|
1353 <td id="LC230" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt<span class="pl-pds">"</span></span> /></td>
|
|
|
1354 </tr>
|
|
|
1355 <tr>
|
|
|
1356 <td id="L231" class="blob-num js-line-number" data-line-number="231"></td>
|
|
|
1357 <td id="LC231" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">repeat</span>></td>
|
|
|
1358 </tr>
|
|
|
1359 <tr>
|
|
|
1360 <td id="L232" class="blob-num js-line-number" data-line-number="232"></td>
|
|
|
1361 <td id="LC232" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td>
|
|
|
1362 </tr>
|
|
|
1363 <tr>
|
|
|
1364 <td id="L233" class="blob-num js-line-number" data-line-number="233"></td>
|
|
|
1365 <td id="LC233" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>bismark<span class="pl-pds">"</span></span> /></td>
|
|
|
1366 </tr>
|
|
|
1367 <tr>
|
|
|
1368 <td id="L234" class="blob-num js-line-number" data-line-number="234"></td>
|
|
|
1369 <td id="LC234" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>bismark_data.txt<span class="pl-pds">"</span></span> /></td>
|
|
|
1370 </tr>
|
|
|
1371 <tr>
|
|
|
1372 <td id="L235" class="blob-num js-line-number" data-line-number="235"></td>
|
|
|
1373 <td id="LC235" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">repeat</span>></td>
|
|
|
1374 </tr>
|
|
|
1375 <tr>
|
|
|
1376 <td id="L236" class="blob-num js-line-number" data-line-number="236"></td>
|
|
|
1377 <td id="LC236" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">repeat</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>results<span class="pl-pds">"</span></span>></td>
|
|
|
1378 </tr>
|
|
|
1379 <tr>
|
|
|
1380 <td id="L237" class="blob-num js-line-number" data-line-number="237"></td>
|
|
|
1381 <td id="LC237" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>software<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>samtools<span class="pl-pds">"</span></span> /></td>
|
|
|
1382 </tr>
|
|
|
1383 <tr>
|
|
|
1384 <td id="L238" class="blob-num js-line-number" data-line-number="238"></td>
|
|
|
1385 <td id="LC238" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>input_file<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>samtools_stats.txt,samtools_flagstat.txt<span class="pl-pds">"</span></span> /></td>
|
|
|
1386 </tr>
|
|
|
1387 <tr>
|
|
|
1388 <td id="L239" class="blob-num js-line-number" data-line-number="239"></td>
|
|
|
1389 <td id="LC239" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">repeat</span>></td>
|
|
|
1390 </tr>
|
|
|
1391 <tr>
|
|
|
1392 <td id="L240" class="blob-num js-line-number" data-line-number="240"></td>
|
|
|
1393 <td id="LC240" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">output</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>html_file<span class="pl-pds">"</span></span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>report_all.html<span class="pl-pds">"</span></span> <span class="pl-e">compare</span>=<span class="pl-s"><span class="pl-pds">"</span>sim_size<span class="pl-pds">"</span></span> <span class="pl-e">delta</span>=<span class="pl-s"><span class="pl-pds">"</span>5000<span class="pl-pds">"</span></span>/></td>
|
|
|
1394 </tr>
|
|
|
1395 <tr>
|
|
|
1396 <td id="L241" class="blob-num js-line-number" data-line-number="241"></td>
|
|
|
1397 <td id="LC241" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">test</span>></td>
|
|
|
1398 </tr>
|
|
|
1399 <tr>
|
|
|
1400 <td id="L242" class="blob-num js-line-number" data-line-number="242"></td>
|
|
|
1401 <td id="LC242" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">tests</span>></td>
|
|
|
1402 </tr>
|
|
|
1403 <tr>
|
|
|
1404 <td id="L243" class="blob-num js-line-number" data-line-number="243"></td>
|
|
|
1405 <td id="LC243" class="blob-code blob-code-inner js-file-line">
|
|
|
1406 </td>
|
|
|
1407 </tr>
|
|
|
1408 <tr>
|
|
|
1409 <td id="L244" class="blob-num js-line-number" data-line-number="244"></td>
|
|
|
1410 <td id="LC244" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">help</span>><span class="pl-s"><span class="pl-pds"><![CDATA[</span></span></td>
|
|
|
1411 </tr>
|
|
|
1412 <tr>
|
|
|
1413 <td id="L245" class="blob-num js-line-number" data-line-number="245"></td>
|
|
|
1414 <td id="LC245" class="blob-code blob-code-inner js-file-line"><span class="pl-s">**What it does**</span></td>
|
|
|
1415 </tr>
|
|
|
1416 <tr>
|
|
|
1417 <td id="L246" class="blob-num js-line-number" data-line-number="246"></td>
|
|
|
1418 <td id="LC246" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
|
|
|
1419 </tr>
|
|
|
1420 <tr>
|
|
|
1421 <td id="L247" class="blob-num js-line-number" data-line-number="247"></td>
|
|
|
1422 <td id="LC247" class="blob-code blob-code-inner js-file-line"><span class="pl-s">MultiQC aggregates results from bioinformatics analyses across many samples into a single report. It takes results of multiple analyses and creates a report that can be viewed as a single beautiful web-page. It's a general use tool, perfect for summarizing the output from numerous bioinformatics tools.</span></td>
|
|
|
1423 </tr>
|
|
|
1424 <tr>
|
|
|
1425 <td id="L248" class="blob-num js-line-number" data-line-number="248"></td>
|
|
|
1426 <td id="LC248" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
|
|
|
1427 </tr>
|
|
|
1428 <tr>
|
|
|
1429 <td id="L249" class="blob-num js-line-number" data-line-number="249"></td>
|
|
|
1430 <td id="LC249" class="blob-code blob-code-inner js-file-line"><span class="pl-s">**Inputs**</span></td>
|
|
|
1431 </tr>
|
|
|
1432 <tr>
|
|
|
1433 <td id="L250" class="blob-num js-line-number" data-line-number="250"></td>
|
|
|
1434 <td id="LC250" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
|
|
|
1435 </tr>
|
|
|
1436 <tr>
|
|
|
1437 <td id="L251" class="blob-num js-line-number" data-line-number="251"></td>
|
|
|
1438 <td id="LC251" class="blob-code blob-code-inner js-file-line"><span class="pl-s">MultiQC takes software output summaries/logs and creates a single report from them. You need to tell the tool which software was used to generate the report. This is done using the **Software name** dropdown. At present the following Galaxy tools produce logs that can used with MultiQC. There are:</span></td>
|
|
|
1439 </tr>
|
|
|
1440 <tr>
|
|
|
1441 <td id="L252" class="blob-num js-line-number" data-line-number="252"></td>
|
|
|
1442 <td id="LC252" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
|
|
|
1443 </tr>
|
|
|
1444 <tr>
|
|
|
1445 <td id="L253" class="blob-num js-line-number" data-line-number="253"></td>
|
|
|
1446 <td id="LC253" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- Fastqc</span></td>
|
|
|
1447 </tr>
|
|
|
1448 <tr>
|
|
|
1449 <td id="L254" class="blob-num js-line-number" data-line-number="254"></td>
|
|
|
1450 <td id="LC254" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- Cutadapt / Trim Galore!</span></td>
|
|
|
1451 </tr>
|
|
|
1452 <tr>
|
|
|
1453 <td id="L255" class="blob-num js-line-number" data-line-number="255"></td>
|
|
|
1454 <td id="LC255" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- Tophat2</span></td>
|
|
|
1455 </tr>
|
|
|
1456 <tr>
|
|
|
1457 <td id="L256" class="blob-num js-line-number" data-line-number="256"></td>
|
|
|
1458 <td id="LC256" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- FeatureCounts (summary file with the column header in the first line or as metadata)</span></td>
|
|
|
1459 </tr>
|
|
|
1460 <tr>
|
|
|
1461 <td id="L257" class="blob-num js-line-number" data-line-number="257"></td>
|
|
|
1462 <td id="LC257" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- Samtools (stats, flagstat, dxstats)</span></td>
|
|
|
1463 </tr>
|
|
|
1464 <tr>
|
|
|
1465 <td id="L258" class="blob-num js-line-number" data-line-number="258"></td>
|
|
|
1466 <td id="LC258" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- Picard (MarkDuplicatesMetrics, CollectGCBiasMetrics, CollectInsertSizeMetrics, CollectAlignmentSummaryMetrics, CollectRnaSeqMetrics)</span></td>
|
|
|
1467 </tr>
|
|
|
1468 <tr>
|
|
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1469 <td id="L259" class="blob-num js-line-number" data-line-number="259"></td>
|
|
|
1470 <td id="LC259" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- Bismark (Alignment report file)</span></td>
|
|
|
1471 </tr>
|
|
|
1472 <tr>
|
|
|
1473 <td id="L260" class="blob-num js-line-number" data-line-number="260"></td>
|
|
|
1474 <td id="LC260" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- Bowtie2 (Metrics file)</span></td>
|
|
|
1475 </tr>
|
|
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1476 <tr>
|
|
|
1477 <td id="L261" class="blob-num js-line-number" data-line-number="261"></td>
|
|
|
1478 <td id="LC261" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- HTSeq-count ("no feature" file; although the "Assigned" metric is always 0)</span></td>
|
|
|
1479 </tr>
|
|
|
1480 <tr>
|
|
|
1481 <td id="L262" class="blob-num js-line-number" data-line-number="262"></td>
|
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|
1482 <td id="LC262" class="blob-code blob-code-inner js-file-line"><span class="pl-s">- RNA STAR (Alignment from Log.final.out, Gene counts from ReadsPerGene.out.tab)</span></td>
|
|
|
1483 </tr>
|
|
|
1484 <tr>
|
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|
1485 <td id="L263" class="blob-num js-line-number" data-line-number="263"></td>
|
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|
1486 <td id="LC263" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
|
|
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1487 </tr>
|
|
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1488 <tr>
|
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1489 <td id="L264" class="blob-num js-line-number" data-line-number="264"></td>
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1490 <td id="LC264" class="blob-code blob-code-inner js-file-line"><span class="pl-s">----</span></td>
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1491 </tr>
|
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1492 <tr>
|
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|
1493 <td id="L265" class="blob-num js-line-number" data-line-number="265"></td>
|
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1494 <td id="LC265" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
|
|
|
1495 </tr>
|
|
|
1496 <tr>
|
|
|
1497 <td id="L266" class="blob-num js-line-number" data-line-number="266"></td>
|
|
|
1498 <td id="LC266" class="blob-code blob-code-inner js-file-line"><span class="pl-s">**Integrated by**</span></td>
|
|
|
1499 </tr>
|
|
|
1500 <tr>
|
|
|
1501 <td id="L267" class="blob-num js-line-number" data-line-number="267"></td>
|
|
|
1502 <td id="LC267" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
|
|
|
1503 </tr>
|
|
|
1504 <tr>
|
|
|
1505 <td id="L268" class="blob-num js-line-number" data-line-number="268"></td>
|
|
|
1506 <td id="LC268" class="blob-code blob-code-inner js-file-line"><span class="pl-s">Cyril Monjeaud and Yvan Le Bras</span></td>
|
|
|
1507 </tr>
|
|
|
1508 <tr>
|
|
|
1509 <td id="L269" class="blob-num js-line-number" data-line-number="269"></td>
|
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|
1510 <td id="LC269" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
|
|
|
1511 </tr>
|
|
|
1512 <tr>
|
|
|
1513 <td id="L270" class="blob-num js-line-number" data-line-number="270"></td>
|
|
|
1514 <td id="LC270" class="blob-code blob-code-inner js-file-line"><span class="pl-s">`EnginesOn &lt;http://engineson.fr/&gt;`_ and Rennes GenOuest Bio-informatics Core Facility</span></td>
|
|
|
1515 </tr>
|
|
|
1516 <tr>
|
|
|
1517 <td id="L271" class="blob-num js-line-number" data-line-number="271"></td>
|
|
|
1518 <td id="LC271" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td>
|
|
|
1519 </tr>
|
|
|
1520 <tr>
|
|
|
1521 <td id="L272" class="blob-num js-line-number" data-line-number="272"></td>
|
|
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1522 <td id="LC272" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> <span class="pl-pds">]]></span></span></<span class="pl-ent">help</span>></td>
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1523 </tr>
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1524 <tr>
|
|
|
1525 <td id="L273" class="blob-num js-line-number" data-line-number="273"></td>
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1526 <td id="LC273" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">citations</span>></td>
|
|
|
1527 </tr>
|
|
|
1528 <tr>
|
|
|
1529 <td id="L274" class="blob-num js-line-number" data-line-number="274"></td>
|
|
|
1530 <td id="LC274" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">citation</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>doi<span class="pl-pds">"</span></span>>10.1093/bioinformatics/btw354</<span class="pl-ent">citation</span>></td>
|
|
|
1531 </tr>
|
|
|
1532 <tr>
|
|
|
1533 <td id="L275" class="blob-num js-line-number" data-line-number="275"></td>
|
|
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1534 <td id="LC275" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">citations</span>></td>
|
|
|
1535 </tr>
|
|
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1536 <tr>
|
|
|
1537 <td id="L276" class="blob-num js-line-number" data-line-number="276"></td>
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1538 <td id="LC276" class="blob-code blob-code-inner js-file-line"></<span class="pl-ent">tool</span>></td>
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1539 </tr>
|
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1540 </table>
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8
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1541
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