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Merge pull request #93 from fls-bioinformatics-core/rnachipintegrator…
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…-3.0.0

Update RnaChipIntegrator tools to version 3.0.0
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@pjbriggs
pjbriggs authored Mar 20, 2024
2 parents 652e807 + 57d7e1f commit e68bd3c
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7 changes: 4 additions & 3 deletions tools/rnachipintegrator/rnachipintegrator_macros.xml
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<macros>
<token name="@VERSION@">1.1.0.0</token>
<token name="@VERSION@">3.0.0+galaxy0</token>
<xml name="requirements">
<requirements>
<requirement type="package" version="2.7">python</requirement>
<requirement type="package" version="1.1.0">rnachipintegrator</requirement>
<requirement type="package" version="3.9">python</requirement>
<requirement type="package" version="3.0.0">rnachipintegrator</requirement>
</requirements>
</xml>
<xml name="version_command">
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label="Gene 'edges' to consider in distance calculations"
help="(--edge)">
<option value="tss" selected="true">TSS only</option>
<option value="tes" selected="true">TES only</option>
<option value="both">Nearest of TSS or TES</option>
</param>
</xml>
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14 changes: 14 additions & 0 deletions tools/rnachipintegrator/rnachipintegrator_wrapper.xml
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<output name="features_per_peak_summary" ftype="tabular"
file="features_per_peak6.summary" />
</test>
<!--
RnaChipIntegrator +name=test +cutoff=130000 +edge=tes +xlsx features.txt peaks.txt
-->
<test>
<param name="features_in" value="features.txt" ftype="tabular" />
<param name="peaks_in" value="peaks.txt" ftype="tabular" />
<param name="cutoff" value="130000" />
<param name="edge" value="tes" />
<output name="xlsx_out" file="peaks7.xlsx" compare="sim_size" />
<output name="peaks_per_feature_out" ftype="tabular"
file="peaks_per_feature7.out" />
<output name="features_per_peak_out" ftype="tabular"
file="features_per_peak7.out" />
</test>
</tests>
<help>

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70 changes: 70 additions & 0 deletions tools/rnachipintegrator/test-data/features_per_peak7.out
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#peak.chr peak.start peak.end gene.id_1 strand_1 TSS_1 TES_1 dist_closest_1 dist_TSS_1 dist_TES_1 direction_1 overlap_gene_1 overlap_promoter_1 gene.id_2 strand_2 TSS_2 TES_2 dist_closest_2 dist_TSS_2 dist_TES_2 direction_2 overlap_gene_2 overlap_promoter_2 gene.id_3 strand_3 TSS_3 TES_3 dist_closest_3 dist_TSS_3 dist_TES_3 direction_3 overlap_gene_3 overlap_promoter_3 gene.id_4 strand_4 TSS_4 TES_4 dist_closest_4 dist_TSS_4 dist_TES_4 direction_4 overlap_gene_4 overlap_promoter_4
chr1 10617233 10617437 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 108747519 108747791 NM_009257_Serpinb5 + 108757652 108779925 9861 9861 32134 U 0 0 NM_009190_Vps4b - 108739123 108665873 8396 8396 81646 U 0 0 NM_027971_Serpinb12 + 108831026 108853655 83235 83235 105864 U 0 0 . . . . . . . . . .
chr1 120760212 120760461 NM_023755_Tcfcp2l1 + 120524515 120655075 105137 235697 105137 D 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 132950929 132951247 NM_008551_Mapkapk2 - 133013820 132950274 0 62573 655 . 1 0 NM_010548_Il10 + 132916424 132921547 29382 34505 29382 D 0 0 NM_145508_Dyrk3 - 133034897 133018921 67674 83650 67674 D 0 0 NM_018750_Rassf5 - 133144761 133072991 121744 193514 121744 D 0 0
chr1 133114860 133115015 NM_001136070_Lgtn + 133049773 133084235 30625 65087 30625 D 0 0 NM_019777_Ikbke - 133176163 133151052 36037 61148 36037 D 0 0 NM_018750_Rassf5 - 133144761 133072991 0 29746 41869 . 1 0 NM_145508_Dyrk3 - 133034897 133018921 79963 79963 95939 U 0 0
chr1 135582677 135582828 NM_001159649_Lax1 - 135586665 135575626 0 3837 7051 . 1 0 NM_213616_Atp2b4 - 135697538 135602265 19437 114710 19437 D 0 0 NM_144530_Zc3h11a - 135557956 135516445 24721 24721 66232 U 0 0 . . . . . . . . . .
chr1 135851853 135852218 NM_054077_Prelp - 135865173 135806855 0 12955 44998 . 1 0 NM_054076_Optc - 135805299 135787973 46554 46554 63880 U 0 0 NM_007570_Btg2 - 135991759 135971251 119033 139541 119033 D 0 0 . . . . . . . . . .
chr1 136956468 136956598 NM_007955_Ptprv - 137029151 137004306 47708 72553 47708 D 0 0 NM_026024_Ube2t + 136857731 136870739 85729 98737 85729 D 0 0 NM_026823_Arl8a + 137043216 137053347 86618 86618 96749 U 0 0 NM_134438_Gpr37l1 - 137069087 137054243 97645 112489 97645 D 0 0
chr1 13829227 13829564 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 138437726 138437860 NM_177643_Zfp281 + 138487073 138526617 49213 49213 88757 U 0 0 NM_026500_Ddx59 + 138242798 138336799 100927 194928 100927 D 0 0 . . . . . . . . . . . . . . . . . . . .
chr1 140381656 140381785 NM_021605_Nek7 - 140516775 140379472 0 134990 2184 . 1 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 145591041 145591176 NM_013835_Trove2 - 145624178 145597816 6640 33002 6640 D 0 0 NM_001038592_Glrx2 + 145585774 145608282 0 5267 17106 . 1 0 NM_019562_Uchl5 + 145623774 145654586 32598 32598 63410 U 0 0 NM_020025_B3galt2 + 145487786 145497516 93525 103255 93525 D 0 0
chr1 154971572 154971673 NM_008485_Lamc2 - 155033557 154969890 0 61884 1682 . 1 0 NM_175460_Nmnat2 + 154802128 154966391 5181 169444 5181 D 0 0 NM_010683_Lamc1 - 155179906 155065803 94130 208233 94130 D 0 0 . . . . . . . . . .
chr1 155123313 155123435 NM_010683_Lamc1 - 155179906 155065803 0 56471 57510 . 1 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 158510523 158510813 NM_023141_Tor3a - 158604477 158583760 72947 93664 72947 D 0 0 NM_145413_Fam20b - 158649180 158608676 97863 138367 97863 D 0 0 . . . . . . . . . . . . . . . . . . . .
chr1 158537267 158537411 NM_023141_Tor3a - 158604477 158583760 46349 67066 46349 D 0 0 NM_145413_Fam20b - 158649180 158608676 71265 111769 71265 D 0 0 . . . . . . . . . . . . . . . . . . . .
chr1 158580638 158580759 NM_023141_Tor3a - 158604477 158583760 3001 23718 3001 D 0 0 NM_145413_Fam20b - 158649180 158608676 27917 68421 27917 D 0 0 . . . . . . . . . . . . . . . . . . . .
chr1 158835251 158835391 NM_028333_Angptl1 + 158769061 158791209 44042 66190 44042 D 0 0 NM_023884_Ralgps2 - 158969600 158734300 0 134209 100951 . 1 0 . . . . . . . . . . . . . . . . . . . .
chr1 159240736 159240866 BC055845_2810025M15Rik + 159342483 159350353 101617 101617 109487 U 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 163827897 163828062 NM_001038619_Dnm3 - 164408155 163902671 74609 580093 74609 D 0 0 NM_010177_Fasl - 163718844 163710820 109053 109053 117077 U 0 0 NM_026078_Pigc + 163860747 163957217 32685 32685 129155 U 0 0 . . . . . . . . . .
chr1 164215623 164215935 NR_002870_Dnm3os + 164119785 164155671 59952 95838 59952 D 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 167222964 167223261 NM_145513_Tiprl - 167183116 167133855 39848 39848 89109 U 0 0 NM_145512_Sft2d2 - 167124549 167104119 98415 98415 118845 U 0 0 . . . . . . . . . . . . . . . . . . . .
chr1 167906284 167906554 NM_001113394_Cd247 + 167711216 167807397 98887 195068 98887 D 0 0 NM_198934_Pou2f1 - 167932753 167804181 0 26199 102103 . 1 0 . . . . . . . . . . . . . . . . . . . .
chr1 170255081 170255260 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 17030405 17030545 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 172620779 172620912 NM_177068_Olfml2b + 172569075 172612915 7864 51704 7864 D 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 172620917 172621080 NM_177068_Olfml2b + 172569075 172612915 8002 51842 8002 D 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 174376470 174376659 NM_029612_Slamf9 + 174392516 174408706 15857 15857 32047 U 0 0 NM_033608_Igsf9 + 174411686 174429005 35027 35027 52346 U 0 0 NM_026234_Pigm + 174306609 174314210 62260 69861 62260 D 0 0 NM_001039484_Kcnj10 + 174258852 174304216 72254 117618 72254 D 0 0
chr1 181061299 181061446 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 182479646 182479905 NM_007415_Parp1 + 182499033 182531385 19128 19128 51480 U 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 185854947 185855105 NM_022019_Dusp10 + 185755009 185899515 0 99938 44410 . 1 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 194258648 194259032 NM_144881_Hhat - 194649833 194320603 61571 390801 61571 D 0 0 NM_010600_Kcnh1 + 194014507 194368391 0 244141 109359 . 1 0 . . . . . . . . . . . . . . . . . . . .
chr1 194645118 194645475 ENSMUST00000057543_A730013G03Rik - 194661397 194659323 13848 15922 13848 D 0 0 NM_198247_Sertad4 - 194693726 194670313 24838 48251 24838 D 0 0 NM_181546_Syt14 - 194861959 194713536 68061 216484 68061 D 0 0 . . . . . . . . . .
chr1 194957396 194957723 NM_145415_AA408296 - 194956446 194918802 950 950 38594 U 0 1 NM_016851_Irf6 + 194979326 194998230 21603 21603 40507 U 0 0 NM_153137_Traf3ip3 - 195027877 195001656 43933 70154 43933 D 0 0 BC055955_A130010J15Rik + 194999663 195004015 41940 41940 46292 U 0 0
chr1 195324443 195324741 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 195330701 195330930 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 195338316 195338616 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 195342728 195342985 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 195384767 195385195 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 197057796 197057843 NM_007758_Cr2 - 197003002 196963005 54794 54794 94791 U 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 24609562 24609623 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 24609923 24609992 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 24730996 24731077 NM_026719_Lmbrd1 + 24820582 24823143 89505 89505 92066 U 0 0 NM_026719_Lmbrd1 + 24593456 24847969 0 137540 116892 . 1 0 . . . . . . . . . . . . . . . . . . . .
chr1 26734195 26734485 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 34206924 34207100 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 36106813 36107058 NM_015818_Hs6st1 + 36125255 36163289 18197 18197 56231 U 0 0 NM_198899_Ugcgl1 - 36301555 36196873 89815 194497 89815 D 0 0 . . . . . . . . . . . . . . . . . . . .
chr1 39492140 39492513 NM_053257_Rpl31 + 39421000 39429094 63046 71140 63046 D 0 0 NM_018775_Tbc1d8 - 39544345 39428350 0 51832 63790 . 1 0 NM_008719_Npas2 + 39250631 39420071 72069 241509 72069 D 0 0 BC049091_D1Bwg0212e + 39592545 39603734 100032 100032 111221 U 0 0
chr1 40325917 40326123 NM_008362_Il1r1 + 40274145 40373439 0 51772 47316 . 1 0 NM_133193_Il1rl2 + 40381454 40447345 55331 55331 121222 U 0 0 . . . . . . . . . . . . . . . . . . . .
chr1 44195449 44195639 NM_144558_Bivm + 44175822 44201615 0 19627 5976 . 1 0 NM_023645_Kdelc1 - 44177102 44143458 18347 18347 51991 U 0 0 NM_011729_Ercc5 + 44204270 44256568 8631 8631 60929 U 0 0 NM_207281_4832428D23Rik - 44515719 44260915 65276 320080 65276 D 0 0
chr1 52625416 52625560 NM_133829_Mfsd6 - 52784383 52702101 76541 158823 76541 D 0 0 NM_001142647_Tmem194b + 52687569 52708760 62009 62009 83200 U 0 0 . . . . . . . . . . . . . . . . . . . .
chr1 54631692 54631815 ENSMUST00000094950_Pgap1 - 54614539 54529849 17153 17153 101843 U 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 55283572 55283675 NM_175439_Mars2 + 55294084 55297625 10409 10409 13950 U 0 0 NM_028713_Rftn2 - 55283748 55227030 0 73 56542 . 1 1 NM_025283_Mobkl3 + 55187734 55211736 71836 95838 71836 D 0 0 . . . . . . . . . .
chr1 63664888 63665018 NM_011780_Adam23 + 63640970 63642850 22038 23918 22038 D 0 0 NM_011780_Adam23 + 63482194 63639230 25658 182694 25658 D 0 0 NM_029696_Mdh1b - 63776894 63745401 80383 111876 80383 D 0 0 . . . . . . . . . .
chr1 72769824 72770056 NM_176980_Ankar - 72747143 72689581 22681 22681 80243 U 0 0 NM_018817_Smarcal1 + 72629842 72679806 90018 139982 90018 D 0 0 NM_008342_Igfbp2 + 72840313 72899038 70257 70257 128982 U 0 0 . . . . . . . . . .
chr1 72770058 72770226 NM_176980_Ankar - 72747143 72689581 22915 22915 80477 U 0 0 NM_018817_Smarcal1 + 72629842 72679806 90252 140216 90252 D 0 0 NM_008342_Igfbp2 + 72840313 72899038 70087 70087 128812 U 0 0 . . . . . . . . . .
chr1 72815517 72815742 NM_008342_Igfbp2 + 72840313 72899038 24571 24571 83296 U 0 0 NM_010518_Igfbp5 - 72921468 72904507 88765 105726 88765 D 0 0 NM_176980_Ankar - 72747143 72689581 68374 68374 125936 U 0 0 . . . . . . . . . .
chr1 75481920 75482054 NM_178884_Obsl1 - 75503218 75482401 347 21164 347 D 0 0 NM_001001565_Chpf - 75476437 75470923 5483 5483 10997 U 0 0 NM_183022_Accn4 + 75447063 75470207 11713 34857 11713 D 0 0 NM_010564_Inha + 75503647 75506924 21593 21593 24870 U 0 0
chr1 77457642 77457791 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 78630893 78631160 NM_026713_Mogat1 + 78496730 78564215 66678 134163 66678 D 0 0 NM_028817_Acsl3 + 78654388 78743434 23228 23228 112274 U 0 0 . . . . . . . . . . . . . . . . . . . .
chr1 88408969 88409267 NM_008801_Pde6d - 88479102 88427331 18064 69835 18064 D 0 0 NM_172974_Cops7b + 88478926 88503950 69659 69659 94683 U 0 0 NM_010933_Nppc - 88567147 88512597 103330 157880 103330 D 0 0 NM_010341_Nmur1 - 88297441 88282479 111528 111528 126490 U 0 0
chr1 89989553 89989714 NM_008299_Dnajb3 - 90102337 90101307 111593 112623 111593 D 0 0 NM_201641_Ugt1a10 + 89922380 90115570 0 67173 125856 . 1 0 . . . . . . . . . . . . . . . . . . . .
chr1 90412932 90413132 NM_008132_Glrp1 - 90406631 90396446 6301 6301 16486 U 0 0 NM_029269_Spp2 + 90303568 90373213 39719 109364 39719 D 0 0 NM_134252_Trpm8 + 90181363 90285482 127450 231569 127450 D 0 0 . . . . . . . . . .
chr1 90592499 90592629 NM_177305_Arl4c - 90617572 90569702 0 24943 22797 . 1 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 91496003 91496145 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 91496155 91496319 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 92070253 92070431 NM_007722_Cxcr7 + 92100063 92112863 29632 29632 42432 U 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chr1 95186508 95186637 NM_178051_Mterfd2 - 95202630 95195779 9142 15993 9142 D 0 0 NM_172463_Sned1 + 95132418 95197642 0 54090 11005 . 1 0 NM_080850_Pask - 95240039 95205357 18720 53402 18720 D 0 0 NM_023200_Ppp1r7 + 95239431 95266345 52794 52794 79708 U 0 0
chr1 9619046 9619167 NM_178399_3110035E14Rik + 9591248 9617222 1824 27798 1824 D 0 0 NM_008651_Mybl1 - 9690280 9635825 16658 71113 16658 D 0 0 NM_175236_Adhfe1 + 9538049 9570746 48300 80997 48300 D 0 0 NM_021511_Rrs1 + 9535513 9537532 81514 83533 81514 D 0 0
chr1 9619175 9619382 NM_178399_3110035E14Rik + 9591248 9617222 1953 27927 1953 D 0 0 NM_008651_Mybl1 - 9690280 9635825 16443 70898 16443 D 0 0 NM_175236_Adhfe1 + 9538049 9570746 48429 81126 48429 D 0 0 NM_021511_Rrs1 + 9535513 9537532 81643 83662 81643 D 0 0
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