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Commit message:
planemo upload commit c1f0c5ceaac87b6b1db12160a8f5b287635db61b |
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added:
test-data/contig1.2bit test-data/contig1.bed.2bit test-data/contig1.both.2bit test-data/contig1.fasta.bed test-data/contig1.fasta.extraspace.out test-data/contig1.fasta.out test-data/contig1.out.2bit tool_dependencies.xml twobit_mask.xml ucsc_macros.xml |
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| diff -r 000000000000 -r fb318f9a36f3 test-data/contig1.2bit |
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| Binary file test-data/contig1.2bit has changed |
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| diff -r 000000000000 -r fb318f9a36f3 test-data/contig1.bed.2bit |
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| Binary file test-data/contig1.bed.2bit has changed |
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| diff -r 000000000000 -r fb318f9a36f3 test-data/contig1.both.2bit |
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| Binary file test-data/contig1.both.2bit has changed |
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| diff -r 000000000000 -r fb318f9a36f3 test-data/contig1.fasta.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contig1.fasta.bed Thu Jun 01 14:10:35 2017 -0400 |
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| @@ -0,0 +1,12 @@ +contig1 9130 9428 trf 163 1.8 164 86 2 438 36 12 13 37 1.82 AAAAAAAATTATATCTTCGGTGTTTTTCAACATACAACCTCCTAAGCTTGGAAATAACATTTCTTAATCAGTTCTGAATTTCGAATTAAATTTTTATCAAAATCGGACAACTATACCATATAGCTGTCATAGGAAGGATTGGATAATTAGTGGTAAAATAATAT +contig1 15707 15757 trf 20 2.5 19 83 9 55 32 12 2 54 1.49 TATATCATTTATATCTCAG +contig1 16261 16302 trf 12 3.4 12 89 0 64 2 36 24 36 1.69 TCCGTCTGTCCG +contig1 23387 23483 trf 45 2.2 45 92 1 158 19 22 30 27 1.98 TCGGCGAAGAAATGTGCCACTTCGGCGGCACTTCTTGGAGTCACT +contig1 23451 23520 trf 24 2.9 24 80 0 75 15 26 27 30 1.96 TTCGGCGACACTTCTTGAAGTCAG +contig1 24200 24233 trf 15 2.2 15 94 0 57 51 12 15 21 1.75 AAACAATGGAATGCT +contig1 29159 29628 trf 162 2.9 160 80 8 518 37 12 11 38 1.80 GGAAAACATGAAATAAAAATTATATCTTTCGTGTTTTTTAACATATACCTTCTAAGCTTGAAAATAACATTTTTTATTTGTTCTGAATTTCGAATTAAATTTTATCAAAATCGGACGACTATATCATATAGCTGTCATAGGAACAATCGGAAAATAAGTA +contig1 37571 37606 trf 8 4.4 8 88 0 52 31 25 42 0 1.55 GACGGACA +contig1 38436 38491 trf 8 6.9 8 79 8 58 0 38 27 34 1.57 TGTCCGTC +contig1 38436 38491 trf 12 4.6 12 81 0 65 0 38 27 34 1.57 TGTCCGTCCGTC +contig1 38436 38491 trf 20 3.1 18 80 17 69 0 38 27 34 1.57 TGTCCGTCTGTCCGTCCG +contig1 43116 43168 trf 2 26.0 2 96 0 95 48 0 1 50 1.12 TA |
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| diff -r 000000000000 -r fb318f9a36f3 test-data/contig1.fasta.extraspace.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contig1.fasta.extraspace.out Thu Jun 01 14:10:35 2017 -0400 |
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| b'@@ -0,0 +1,103 @@\n+ SW perc perc perc query position in query matching repeat position in repeat\n+score div. del. ins. sequence begin end (left) repeat class/family begin end (left) ID\n+\n+ 2239 13.1 11.2 0.7 contig1 7 452 (44727) C rnd-4_family-146 RC/Helitron (320) 924 432 1 \n+ 1795 13.4 12.0 1.2 contig1 224 631 (44548) + rnd-1_family-0 RC/Helitron 9 460 (0) 2 *\n+ 309 28.3 5.6 4.0 contig1 5522 5646 (39533) C rnd-5_family-2216 RC/Helitron (185) 457 331 3 \n+ 565 19.4 1.6 1.6 contig1 6493 6618 (38561) + rnd-1_family-2 RC/Helitron 2 127 (29) 4 \n+ 267 9.8 13.7 0.0 contig1 6685 6735 (38444) + rnd-1_family-31 RC/Helitron 1 58 (0) 5 *\n+ 2033 5.7 4.2 0.0 contig1 6702 6963 (38216) + rnd-4_family-146 RC/Helitron 44 316 (928) 6 *\n+ 2466 14.1 4.2 2.8 contig1 6768 7489 (37690) C rnd-4_family-146 RC/Helitron (0) 1244 351 7 \n+ 317 13.8 0.0 0.0 contig1 7498 7555 (37624) + rnd-1_family-99 Unknown 82 139 (1) 8 \n+ 271 10.9 0.0 0.0 contig1 7516 7561 (37618) C rnd-1_family-99 Unknown (86) 54 9 9 *\n+ 639 13.4 0.0 0.0 contig1 7560 7656 (37523) + rnd-1_family-34 Unknown 92 188 (0) 10 *\n+ 1471 16.2 3.0 0.0 contig1 7653 7917 (37262) C rnd-5_family-8111 Unknown (129) 273 1 11 \n+ 465 22.9 3.1 6.2 contig1 8032 8252 (36927) C rnd-1_family-4 RC/Helitron (0) 196 1 12 *\n+ 793 4.2 0.0 0.0 contig1 8234 8328 (36851) C rnd-1_family-7 RC/Helitron (2) 140 46 13 \n+ 747 10.1 7.6 0.0 contig1 8325 8443 (36736) C rnd-1_family-2 RC/Helitron (25) 131 4 14 *\n+ 1621 12.6 5.3 2.8 contig1 8906 9259 (35920) + rnd-4_family-146 RC/Helitron 72 319 (925) 15 *\n+ 2224 12.4 8.7 2.1 contig1 9105 9541 (35638) C rnd-4_family-146 RC/Helitron (207) 1037 572 16 *\n+ 2442 7.1 11.9 1.7 contig1 9294 9706 (35473) + rnd-1_family-0 RC/Helitron 6 460 (0) 17 \n+ 308 7.0 0.0 0.0 contig1 9954 9996 (35183) + rnd-5_family-8111 Unknown 2 44 (358) 18 \n+ 660 18.8 8.3 0.0 contig1 10019 10151 (35028) + rnd-5_family-8111 Unknown 186 329 (73) 19 \n+ 1661 18.1 9.3 3.6 contig1 10159 10576 (34603) C rnd-4_family-306 Unknown (78) 468 27 20 \n+ 1521 12.2 14.9 1.3 contig1 10577 10891 (34288) C rnd-4_family-146 RC/Helitron (532) 712 355 21 \n+ 555 10.0 0.0 0.0 contig1 10899 10978 (34201) + rnd-1_family-211 Unknown 2 81 (20) 22 \n+ 356 15.7 30.0 0.0 contig1 11135 11262 (33917) C rnd-4_family-146 RC/Helitron (1085) 159 2 21 \n+ 307 25.5 4.2 2.1 contig1 11920 12015 (33164) C rnd-4_family-1925 Unknown (0) 260 163 23 \n+ 436 23.6 0.0 1.1 contig1 13661 13750 (31429) + rnd-5_family-288 Unknown 49 137 (340) 24 \n+ 313 24.7 6.4 1.1 contig1 14089 14182 (30997) + rnd-5_family-288 Unknown 163 261 (216) 24 \n+ 524 13.0 1.0 1.0 contig1 14660 14760 (30419) + rnd-5_family-128 Unknown 92 192 (167) 25 \n+ 350 10.0 0.0 0.0 contig1 14801 14850 (30329) C rnd-1_family-420 Unknown (84) 50 1 26 \n+ 305 18.9 2.6 3.9 contig1 15797 15873 (29306) C rnd-5_family-3538 Unknown (2) 178 103 27 \n+ 536 12.4 22.8 2.3 contig1 15946 16116 (29063) + rnd-5_family-107 RC/Helitron 291 496 (99) 28 \n+ 329 10.4 0.0 0.0 contig1 16127 16174 (29005) + rnd-1_family-40 Unknown 1 48 (0) 29 *\n+ 1758 8.6 0.8 9.2 c'..b'itron 1 317 (927) 63 *\n+ 4453 9.9 0.6 0.7 contig1 29146 29828 (15351) C rnd-4_family-146 RC/Helitron (208) 1036 355 64 \n+ 283 15.6 0.0 0.0 contig1 30091 30135 (15044) + rnd-4_family-108 RC/Helitron 66 110 (343) 65 \n+ 753 22.9 11.4 3.3 contig1 30179 30449 (14730) + rnd-5_family-2216 RC/Helitron 310 602 (40) 66 \n+ 367 22.4 3.6 4.5 contig1 30475 30586 (14593) + rnd-1_family-3 RC/Helitron 80 190 (63) 67 \n+ 315 8.2 2.0 0.0 contig1 30564 30612 (14567) + rnd-1_family-4 RC/Helitron 90 139 (57) 68 *\n+ 327 28.2 4.8 5.5 contig1 30861 31025 (14154) + rnd-4_family-1925 Unknown 97 260 (0) 69 \n+ 478 12.2 13.3 0.0 contig1 35887 35976 (9203) C rnd-5_family-2216 RC/Helitron (14) 628 527 70 \n+ 465 15.6 3.1 14.2 contig1 36021 36147 (9032) C rnd-4_family-108 RC/Helitron (307) 146 34 71 \n+ 297 20.6 1.4 0.0 contig1 36361 36433 (8746) + rnd-3_family-10 DNA/TcMar-Mariner 1305 1378 (43) 72 \n+ 285 21.0 6.2 0.0 contig1 36376 36456 (8723) + rnd-2_family-32 RC/Helitron 260 345 (398) 73 *\n+ 305 11.8 2.0 0.0 contig1 37138 37188 (7991) C rnd-1_family-0 RC/Helitron (395) 65 14 74 \n+ 906 10.8 12.7 0.6 contig1 37201 37358 (7821) C rnd-4_family-146 RC/Helitron (1052) 192 16 75 \n+ 285 11.6 0.0 0.0 contig1 37378 37420 (7759) C rnd-5_family-2216 RC/Helitron (17) 625 583 76 *\n+ 795 15.9 4.8 1.1 contig1 37413 37631 (7548) C rnd-2_family-29 RC/Helitron (306) 253 2 70 \n+ 807 5.7 1.9 0.0 contig1 37667 37772 (7407) C rnd-1_family-53 Unknown (0) 112 5 77 \n+ 430 13.6 4.5 1.1 contig1 37848 37936 (7243) C rnd-2_family-32 RC/Helitron (74) 669 578 78 *\n+ 1235 8.6 2.1 0.5 contig1 37935 38122 (7057) + rnd-4_family-146 RC/Helitron 674 864 (380) 79 \n+ 1194 16.9 24.0 0.8 contig1 38004 38361 (6818) C rnd-2_family-32 RC/Helitron (149) 594 154 78 *\n+ 1598 10.2 5.5 8.4 contig1 38362 38831 (6348) + rnd-4_family-146 RC/Helitron 43 356 (888) 80 \n+ 1291 9.2 0.0 0.0 contig1 38770 38954 (6225) C rnd-2_family-32 RC/Helitron (83) 660 476 81 *\n+ 693 8.0 5.3 0.9 contig1 39581 39694 (5485) + rnd-3_family-10 DNA/TcMar-Mariner 1296 1414 (7) 82 *\n+ 2674 10.1 0.7 1.9 contig1 39636 40096 (5083) + rnd-4_family-146 RC/Helitron 248 763 (481) 83 \n+ 1535 4.9 0.0 1.6 contig1 40095 40281 (4898) C rnd-2_family-19 RC/Helitron (43) 184 1 84 *\n+ 2609 13.1 4.0 0.4 contig1 40279 40731 (4448) C rnd-4_family-146 RC/Helitron (235) 1009 541 85 *\n+ 2729 8.5 4.0 0.2 contig1 40439 40861 (4318) + rnd-1_family-0 RC/Helitron 21 459 (1) 86 \n+ 349 26.1 0.8 2.5 contig1 42871 42992 (2187) + rnd-4_family-146 RC/Helitron 539 658 (586) 87 \n+ 318 21.6 15.9 0.0 contig1 43030 43117 (2062) C rnd-4_family-146 RC/Helitron (1073) 171 70 85 \n+ 260 23.5 0.0 1.4 contig1 43192 43260 (1919) C rnd-1_family-0 RC/Helitron (281) 179 112 88 \n+ 446 14.5 0.0 0.0 contig1 43299 43367 (1812) C rnd-1_family-53 Unknown (2) 110 42 89 \n+ 421 21.4 12.7 0.0 contig1 43323 43448 (1731) + rnd-5_family-8111 Unknown 105 246 (156) 90 *\n+ 431 16.2 0.0 0.0 contig1 43482 43561 (1618) C rnd-1_family-99 Unknown (56) 84 5 91 *\n+ 595 14.3 0.0 0.0 contig1 43533 43630 (1549) C rnd-1_family-50 Unknown (0) 128 31 92 \n+ 1122 16.0 6.8 0.0 contig1 43634 43839 (1340) + rnd-4_family-146 RC/Helitron 64 283 (961) 93 \n' |
| b |
| diff -r 000000000000 -r fb318f9a36f3 test-data/contig1.fasta.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contig1.fasta.out Thu Jun 01 14:10:35 2017 -0400 |
| b |
| b'@@ -0,0 +1,103 @@\n+ SW perc perc perc query position in query matching repeat position in repeat\n+score div. del. ins. sequence begin end (left) repeat class/family begin end (left) ID\n+\n+ 2239 13.1 11.2 0.7 contig1 7 452 (44727) C rnd-4_family-146 RC/Helitron (320) 924 432 1 \n+ 1795 13.4 12.0 1.2 contig1 224 631 (44548) + rnd-1_family-0 RC/Helitron 9 460 (0) 2 *\n+ 309 28.3 5.6 4.0 contig1 5522 5646 (39533) C rnd-5_family-2216 RC/Helitron (185) 457 331 3 \n+ 565 19.4 1.6 1.6 contig1 6493 6618 (38561) + rnd-1_family-2 RC/Helitron 2 127 (29) 4 \n+ 267 9.8 13.7 0.0 contig1 6685 6735 (38444) + rnd-1_family-31 RC/Helitron 1 58 (0) 5 *\n+ 2033 5.7 4.2 0.0 contig1 6702 6963 (38216) + rnd-4_family-146 RC/Helitron 44 316 (928) 6 *\n+ 2466 14.1 4.2 2.8 contig1 6768 7489 (37690) C rnd-4_family-146 RC/Helitron (0) 1244 351 7 \n+ 317 13.8 0.0 0.0 contig1 7498 7555 (37624) + rnd-1_family-99 Unknown 82 139 (1) 8 \n+ 271 10.9 0.0 0.0 contig1 7516 7561 (37618) C rnd-1_family-99 Unknown (86) 54 9 9 *\n+ 639 13.4 0.0 0.0 contig1 7560 7656 (37523) + rnd-1_family-34 Unknown 92 188 (0) 10 *\n+ 1471 16.2 3.0 0.0 contig1 7653 7917 (37262) C rnd-5_family-8111 Unknown (129) 273 1 11 \n+ 465 22.9 3.1 6.2 contig1 8032 8252 (36927) C rnd-1_family-4 RC/Helitron (0) 196 1 12 *\n+ 793 4.2 0.0 0.0 contig1 8234 8328 (36851) C rnd-1_family-7 RC/Helitron (2) 140 46 13 \n+ 747 10.1 7.6 0.0 contig1 8325 8443 (36736) C rnd-1_family-2 RC/Helitron (25) 131 4 14 *\n+ 1621 12.6 5.3 2.8 contig1 8906 9259 (35920) + rnd-4_family-146 RC/Helitron 72 319 (925) 15 *\n+ 2224 12.4 8.7 2.1 contig1 9105 9541 (35638) C rnd-4_family-146 RC/Helitron (207) 1037 572 16 *\n+ 2442 7.1 11.9 1.7 contig1 9294 9706 (35473) + rnd-1_family-0 RC/Helitron 6 460 (0) 17 \n+ 308 7.0 0.0 0.0 contig1 9954 9996 (35183) + rnd-5_family-8111 Unknown 2 44 (358) 18 \n+ 660 18.8 8.3 0.0 contig1 10019 10151 (35028) + rnd-5_family-8111 Unknown 186 329 (73) 19 \n+ 1661 18.1 9.3 3.6 contig1 10159 10576 (34603) C rnd-4_family-306 Unknown (78) 468 27 20 \n+ 1521 12.2 14.9 1.3 contig1 10577 10891 (34288) C rnd-4_family-146 RC/Helitron (532) 712 355 21 \n+ 555 10.0 0.0 0.0 contig1 10899 10978 (34201) + rnd-1_family-211 Unknown 2 81 (20) 22 \n+ 356 15.7 30.0 0.0 contig1 11135 11262 (33917) C rnd-4_family-146 RC/Helitron (1085) 159 2 21 \n+ 307 25.5 4.2 2.1 contig1 11920 12015 (33164) C rnd-4_family-1925 Unknown (0) 260 163 23 \n+ 436 23.6 0.0 1.1 contig1 13661 13750 (31429) + rnd-5_family-288 Unknown 49 137 (340) 24 \n+ 313 24.7 6.4 1.1 contig1 14089 14182 (30997) + rnd-5_family-288 Unknown 163 261 (216) 24 \n+ 524 13.0 1.0 1.0 contig1 14660 14760 (30419) + rnd-5_family-128 Unknown 92 192 (167) 25 \n+ 350 10.0 0.0 0.0 contig1 14801 14850 (30329) C rnd-1_family-420 Unknown (84) 50 1 26 \n+ 305 18.9 2.6 3.9 contig1 15797 15873 (29306) C rnd-5_family-3538 Unknown (2) 178 103 27 \n+ 536 12.4 22.8 2.3 contig1 15946 16116 (29063) + rnd-5_family-107 RC/Helitron 291 496 (99) 28 \n+ 329 10.4 0.0 0.0 contig1 16127 16174 (29005) + rnd-1_family-40 Unknown 1 48 (0) 29 *\n+ 1758 8.6 0.8 9.2 co'..b'itron 1 317 (927) 63 *\n+ 4453 9.9 0.6 0.7 contig1 29146 29828 (15351) C rnd-4_family-146 RC/Helitron (208) 1036 355 64 \n+ 283 15.6 0.0 0.0 contig1 30091 30135 (15044) + rnd-4_family-108 RC/Helitron 66 110 (343) 65 \n+ 753 22.9 11.4 3.3 contig1 30179 30449 (14730) + rnd-5_family-2216 RC/Helitron 310 602 (40) 66 \n+ 367 22.4 3.6 4.5 contig1 30475 30586 (14593) + rnd-1_family-3 RC/Helitron 80 190 (63) 67 \n+ 315 8.2 2.0 0.0 contig1 30564 30612 (14567) + rnd-1_family-4 RC/Helitron 90 139 (57) 68 *\n+ 327 28.2 4.8 5.5 contig1 30861 31025 (14154) + rnd-4_family-1925 Unknown 97 260 (0) 69 \n+ 478 12.2 13.3 0.0 contig1 35887 35976 (9203) C rnd-5_family-2216 RC/Helitron (14) 628 527 70 \n+ 465 15.6 3.1 14.2 contig1 36021 36147 (9032) C rnd-4_family-108 RC/Helitron (307) 146 34 71 \n+ 297 20.6 1.4 0.0 contig1 36361 36433 (8746) + rnd-3_family-10 DNA/TcMar-Mariner 1305 1378 (43) 72 \n+ 285 21.0 6.2 0.0 contig1 36376 36456 (8723) + rnd-2_family-32 RC/Helitron 260 345 (398) 73 *\n+ 305 11.8 2.0 0.0 contig1 37138 37188 (7991) C rnd-1_family-0 RC/Helitron (395) 65 14 74 \n+ 906 10.8 12.7 0.6 contig1 37201 37358 (7821) C rnd-4_family-146 RC/Helitron (1052) 192 16 75 \n+ 285 11.6 0.0 0.0 contig1 37378 37420 (7759) C rnd-5_family-2216 RC/Helitron (17) 625 583 76 *\n+ 795 15.9 4.8 1.1 contig1 37413 37631 (7548) C rnd-2_family-29 RC/Helitron (306) 253 2 70 \n+ 807 5.7 1.9 0.0 contig1 37667 37772 (7407) C rnd-1_family-53 Unknown (0) 112 5 77 \n+ 430 13.6 4.5 1.1 contig1 37848 37936 (7243) C rnd-2_family-32 RC/Helitron (74) 669 578 78 *\n+ 1235 8.6 2.1 0.5 contig1 37935 38122 (7057) + rnd-4_family-146 RC/Helitron 674 864 (380) 79 \n+ 1194 16.9 24.0 0.8 contig1 38004 38361 (6818) C rnd-2_family-32 RC/Helitron (149) 594 154 78 *\n+ 1598 10.2 5.5 8.4 contig1 38362 38831 (6348) + rnd-4_family-146 RC/Helitron 43 356 (888) 80 \n+ 1291 9.2 0.0 0.0 contig1 38770 38954 (6225) C rnd-2_family-32 RC/Helitron (83) 660 476 81 *\n+ 693 8.0 5.3 0.9 contig1 39581 39694 (5485) + rnd-3_family-10 DNA/TcMar-Mariner 1296 1414 (7) 82 *\n+ 2674 10.1 0.7 1.9 contig1 39636 40096 (5083) + rnd-4_family-146 RC/Helitron 248 763 (481) 83 \n+ 1535 4.9 0.0 1.6 contig1 40095 40281 (4898) C rnd-2_family-19 RC/Helitron (43) 184 1 84 *\n+ 2609 13.1 4.0 0.4 contig1 40279 40731 (4448) C rnd-4_family-146 RC/Helitron (235) 1009 541 85 *\n+ 2729 8.5 4.0 0.2 contig1 40439 40861 (4318) + rnd-1_family-0 RC/Helitron 21 459 (1) 86 \n+ 349 26.1 0.8 2.5 contig1 42871 42992 (2187) + rnd-4_family-146 RC/Helitron 539 658 (586) 87 \n+ 318 21.6 15.9 0.0 contig1 43030 43117 (2062) C rnd-4_family-146 RC/Helitron (1073) 171 70 85 \n+ 260 23.5 0.0 1.4 contig1 43192 43260 (1919) C rnd-1_family-0 RC/Helitron (281) 179 112 88 \n+ 446 14.5 0.0 0.0 contig1 43299 43367 (1812) C rnd-1_family-53 Unknown (2) 110 42 89 \n+ 421 21.4 12.7 0.0 contig1 43323 43448 (1731) + rnd-5_family-8111 Unknown 105 246 (156) 90 *\n+ 431 16.2 0.0 0.0 contig1 43482 43561 (1618) C rnd-1_family-99 Unknown (56) 84 5 91 *\n+ 595 14.3 0.0 0.0 contig1 43533 43630 (1549) C rnd-1_family-50 Unknown (0) 128 31 92 \n+ 1122 16.0 6.8 0.0 contig1 43634 43839 (1340) + rnd-4_family-146 RC/Helitron 64 283 (961) 93 \n' |
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| diff -r 000000000000 -r fb318f9a36f3 test-data/contig1.out.2bit |
| b |
| Binary file test-data/contig1.out.2bit has changed |
| b |
| diff -r 000000000000 -r fb318f9a36f3 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Jun 01 14:10:35 2017 -0400 |
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| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="ucsc_twobit" version="340"> + <repository changeset_revision="f03dc0347e70" name="package_ucsc_twobit_340" owner="yating-l" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |
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| diff -r 000000000000 -r fb318f9a36f3 twobit_mask.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/twobit_mask.xml Thu Jun 01 14:10:35 2017 -0400 |
| [ |
| @@ -0,0 +1,116 @@ +<?xml version="1.0"?> +<tool id="twobit_mask" name="twoBitMask" version="1.0"> + <description>Apply repeat masking to a twoBit file</description> + + <macros> + <import>ucsc_macros.xml</import> + </macros> + + <expand macro="requirements_twobit" /> + + <command detect_errors="exit_code"> +<![CDATA[ + #if str($maskfile_type.maskfile_type_selector) == "out": + ## twoBitMask expects the first column of the RepeatMasker header to + ## contain only three leading spaces. RepeatMasker output with large + ## SW scores could contain more leading spaces. + + awk '{ sub(/^\s+SW/, " SW"); print }' "${out_maskfile}" | + twoBitMask + ${add_mask} + -type=.out + "${twobit_input}" stdin "${twobit_output}" + #else: + ## The BED Output from TRF is in bed4+ format, but twoBitMask + ## only uses the first three fields of a BED file. + ## The extra columns result in a warning from twoBitMask + + awk 'BEGIN { OFS="\t" } { print $1, $2, $3 }' "${bed_maskfile}" | + twoBitMask + ${add_mask} + -type=.bed + "${twobit_input}" stdin "${twobit_output}" + #end if +]]> + </command> + <inputs> + <param name="twobit_input" type="data" format="twobit" label="twoBit input file" /> + + <param name="add_mask" type="boolean" checked="true" + truevalue="-add" falsevalue="" + label="Keep pre-existing masking" + help="-add" /> + + <conditional name="maskfile_type"> + <param name="maskfile_type_selector" type="select" + label="Choose the type of mask file" + help="Mask file can be a RepeatMasker .out file or a BED file"> + <option value="out">RepeatMasker .out file</option> + <option value="bed" selected="true">BED file</option> + </param> + + <when value="out"> + <param name="out_maskfile" type="data" format="txt" + label="Mask file in RepeatMasker .out format" /> + </when> + + <when value="bed"> + <param name="bed_maskfile" type="data" format="bed" + label="Mask file in BED format" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="twobit_output" format="twobit" /> + </outputs> + <tests> + <test> + <!-- Test standard RepeatMasker .out file --> + <param name="twobit_input" value="contig1.2bit" ftype="twobit" /> + <param name="maskfile_type_selector" value="out" /> + <param name="out_maskfile" value="contig1.fasta.out" /> + <output name="twobit_output" file="contig1.out.2bit" /> + </test> + <test> + <!-- Test RepeatMasker .out file with extra space in header --> + <param name="twobit_input" value="contig1.2bit" ftype="twobit" /> + <param name="maskfile_type_selector" value="out" /> + <param name="out_maskfile" value="contig1.fasta.extraspace.out" /> + <output name="twobit_output" file="contig1.out.2bit" /> + </test> + <test> + <!-- Test TRF .bed output --> + <param name="twobit_input" value="contig1.2bit" ftype="twobit" /> + <param name="maskfile_type_selector" value="bed" /> + <param name="bed_maskfile" value="contig1.fasta.bed" ftype="bed" /> + <output name="twobit_output" file="contig1.bed.2bit" /> + </test> + <test> + <!-- Test keep pre-existing masking --> + <param name="twobit_input" value="contig1.bed.2bit" ftype="twobit" /> + <param name="maskfile_type_selector" value="out" /> + <param name="out_maskfile" value="contig1.fasta.out" /> + <output name="twobit_output" file="contig1.both.2bit" /> + </test> + <test> + <!-- Test ignore pre-existing masking --> + <param name="twobit_input" value="contig1.bed.2bit" ftype="twobit" /> + <param name="maskfile_type_selector" value="out" /> + <param name="out_maskfile" value="contig1.fasta.out" /> + <param name="add_mask" value="" /> + <output name="twobit_output" file="contig1.out.2bit" /> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +twoBitMask applies a mask to a twoBit file based on repeat information +from a `RepeatMasker <http://www.repeatmasker.org/>`_ .out file or +a BED file (e.g., from +`Tandem Repeats Finder <https://tandem.bu.edu/trf/trf.html>`_). + + ]]></help> + + <expand macro="citations" /> +</tool> |
| b |
| diff -r 000000000000 -r fb318f9a36f3 ucsc_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ucsc_macros.xml Thu Jun 01 14:10:35 2017 -0400 |
| [ |
| @@ -0,0 +1,44 @@ +<macros> + <xml name="requirements_twobit"> + <requirements> + <requirement type="package" version="340">ucsc_twobit</requirement> + <yield /> + </requirements> + </xml> + <xml name="environment_LC_COLLATE"> + <environment_variables> + <!-- Sort uppercase letters before lowercase (required by UCSC tools) --> + <environment_variable name="LC_COLLATE">C</environment_variable> + <yield /> + </environment_variables> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @article{Kent01062002, +author = {Kent, W. James and Sugnet, Charles W. and Furey, Terrence S. and Roskin, Krishna M. and Pringle, Tom H. and Zahler, Alan M. and Haussler, and David}, +title = {The Human Genome Browser at UCSC}, +volume = {12}, +number = {6}, +pages = {996-1006}, +year = {2002}, +doi = {10.1101/gr.229102}, +URL = {http://genome.cshlp.org/content/12/6/996.abstract}, +eprint = {http://genome.cshlp.org/content/12/6/996.full.pdf+html}, +journal = {Genome Research} +} + </citation> + <yield /> + </citations> + </xml> + + <token name="@OPTIONAL_PARAM_FUNC@"> +<![CDATA[ + #def optional_param($_flag, $_flag_value, $_sep="=") + #if str($_flag_value) and str($_flag_value).strip(): + ${_flag}${_sep}${_flag_value} + #end if + #end def +]]> + </token> +</macros> |