Mercurial > repos > saskia-hiltemann > ireport_devel

comparison createHTML.sh @ 3:945e72d0e723 draft

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author saskia-hiltemann
date Wed, 15 Jul 2015 09:21:59 -0400
parents d582e2cd3e13
children 363cd315d0e9
comparison
equal deleted inserted replaced
2:43a134bbc2da 3:945e72d0e723
430 430
431 iframecount=$[$iframecount+1] 431 iframecount=$[$iframecount+1]
432 if [ $fancy == "Y" ] 432 if [ $fancy == "Y" ]
433 then 433 then
434 perl ${repositorypath}/tsv2html.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html 434 perl ${repositorypath}/tsv2html.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html
435 contentline="${contentline}\n<iframe class=\"invisibleframe fancyiframe\" id=\"$iframeid\" src=\"htmltable_${fname}.html\" width=\"100%\" style=\"height: 350px; min-height: ${minh}px !important; overflow-y: hidden; overflow-x: scroll\" ></iframe>" 435 contentline="${contentline}\n<iframe class=\"invisibleframe fancyiframe\" id=\"$iframeid\" src=\"htmltable_${fname}.html\" width=\"100%\" style=\"height: 760px; min-height: ${minh}px !important; overflow-y: hidden; overflow-x: scroll\" ></iframe>"
436 iframecount=$[$iframecount+1] 436 iframecount=$[$iframecount+1]
437 else 437 else
438 perl ${repositorypath}/tsv2html_simple.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html 438 perl ${repositorypath}/tsv2html_simple.pl < ${tsvfile}2 > ${galaxypath}/htmltable_${fname}.html
439 contentline="${contentline}\n<iframe class=\"unfancyiframe invisibleframe\" id=\"$iframeid\" src=\"htmltable_${fname}.html\" scrolling=\"no\" style=\"min-width: ${minw}px; min-height: ${minh}px !important; max-width: 100%; vertical-align: top;\" onload=\"resizeIframe(this)\"></iframe>" 439 contentline="${contentline}\n<iframe class=\"unfancyiframe invisibleframe\" id=\"$iframeid\" src=\"htmltable_${fname}.html\" scrolling=\"no\" style=\"min-width: ${minw}px; min-height: ${minh}px !important; max-width: 100%; vertical-align: top;\" onload=\"resizeIframe(this)\"></iframe>"
440 iframecount=$[$iframecount+1] 440 iframecount=$[$iframecount+1]
626 samtools index "${galaxypath}/${newgbfilename}" 626 samtools index "${galaxypath}/${newgbfilename}"
627 627
628 userTracks="${userTracks}, 628 userTracks="${userTracks},
629 {name: '${gbfilelabel}', 629 {name: '${gbfilelabel}',
630 bamURI: '${servername}/datasets/${apiid}/display/${newgbfilename}'} 630 bamURI: '${servername}/datasets/${apiid}/display/${newgbfilename}'}
631 "
632
633 fi
634
635 if [[ $ftype == "bigbed" ]]
636 then
637 newgbfilename="${fname}.bigbed"
638
639 cp ${gbfilename} "${galaxypath}/${newgbfilename}"
640 #bgzip "${galaxypath}/${newgbfilename}"
641 #tabix -f -p bed "${galaxypath}/${newgbfilename}.gz"
642
643 userTracks="${userTracks},
644 {name: '${gbfilelabel}',
645 bwgURI: '${servername}/datasets/${apiid}/display/${newgbfilename}'}
646 " 631 "
647 632
648 fi 633 fi
649 634
650 if [[ $ftype == "bedtabix" ]] 635 if [[ $ftype == "bedtabix" ]]