# HG changeset patch
# User yating-l
# Date 1496340635 14400
# Node ID fb318f9a36f34e44fdb0915bf602531fab6f041e

planemo upload commit c1f0c5ceaac87b6b1db12160a8f5b287635db61b

diff -r 000000000000 -r fb318f9a36f3 test-data/contig1.2bit
Binary file test-data/contig1.2bit has changed
diff -r 000000000000 -r fb318f9a36f3 test-data/contig1.bed.2bit
Binary file test-data/contig1.bed.2bit has changed
diff -r 000000000000 -r fb318f9a36f3 test-data/contig1.both.2bit
Binary file test-data/contig1.both.2bit has changed
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
@@ -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
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
@@ -0,0 +1,103 @@
+    SW   perc perc perc  query     position in query     matching          repeat              position in repeat
+score   div. del. ins.  sequence  begin end    (left)   repeat            class/family      begin  end    (left)  ID
+
+ 2239   13.1 11.2  0.7  contig1       7   452 (44727) C rnd-4_family-146  RC/Helitron        (320)    924    432   1  
+ 1795   13.4 12.0  1.2  contig1     224   631 (44548) + rnd-1_family-0    RC/Helitron            9    460    (0)   2 *
+  309   28.3  5.6  4.0  contig1    5522  5646 (39533) C rnd-5_family-2216 RC/Helitron        (185)    457    331   3  
+  565   19.4  1.6  1.6  contig1    6493  6618 (38561) + rnd-1_family-2    RC/Helitron            2    127   (29)   4  
+  267    9.8 13.7  0.0  contig1    6685  6735 (38444) + rnd-1_family-31   RC/Helitron            1     58    (0)   5 *
+ 2033    5.7  4.2  0.0  contig1    6702  6963 (38216) + rnd-4_family-146  RC/Helitron           44    316  (928)   6 *
+ 2466   14.1  4.2  2.8  contig1    6768  7489 (37690) C rnd-4_family-146  RC/Helitron          (0)   1244    351   7  
+  317   13.8  0.0  0.0  contig1    7498  7555 (37624) + rnd-1_family-99   Unknown               82    139    (1)   8  
+  271   10.9  0.0  0.0  contig1    7516  7561 (37618) C rnd-1_family-99   Unknown             (86)     54      9   9 *
+  639   13.4  0.0  0.0  contig1    7560  7656 (37523) + rnd-1_family-34   Unknown               92    188    (0)  10 *
+ 1471   16.2  3.0  0.0  contig1    7653  7917 (37262) C rnd-5_family-8111 Unknown            (129)    273      1  11  
+  465   22.9  3.1  6.2  contig1    8032  8252 (36927) C rnd-1_family-4    RC/Helitron          (0)    196      1  12 *
+  793    4.2  0.0  0.0  contig1    8234  8328 (36851) C rnd-1_family-7    RC/Helitron          (2)    140     46  13  
+  747   10.1  7.6  0.0  contig1    8325  8443 (36736) C rnd-1_family-2    RC/Helitron         (25)    131      4  14 *
+ 1621   12.6  5.3  2.8  contig1    8906  9259 (35920) + rnd-4_family-146  RC/Helitron           72    319  (925)  15 *
+ 2224   12.4  8.7  2.1  contig1    9105  9541 (35638) C rnd-4_family-146  RC/Helitron        (207)   1037    572  16 *
+ 2442    7.1 11.9  1.7  contig1    9294  9706 (35473) + rnd-1_family-0    RC/Helitron            6    460    (0)  17  
+  308    7.0  0.0  0.0  contig1    9954  9996 (35183) + rnd-5_family-8111 Unknown                2     44  (358)  18  
+  660   18.8  8.3  0.0  contig1   10019 10151 (35028) + rnd-5_family-8111 Unknown              186    329   (73)  19  
+ 1661   18.1  9.3  3.6  contig1   10159 10576 (34603) C rnd-4_family-306  Unknown             (78)    468     27  20  
+ 1521   12.2 14.9  1.3  contig1   10577 10891 (34288) C rnd-4_family-146  RC/Helitron        (532)    712    355  21  
+  555   10.0  0.0  0.0  contig1   10899 10978 (34201) + rnd-1_family-211  Unknown                2     81   (20)  22  
+  356   15.7 30.0  0.0  contig1   11135 11262 (33917) C rnd-4_family-146  RC/Helitron       (1085)    159      2  21  
+  307   25.5  4.2  2.1  contig1   11920 12015 (33164) C rnd-4_family-1925 Unknown              (0)    260    163  23  
+  436   23.6  0.0  1.1  contig1   13661 13750 (31429) + rnd-5_family-288  Unknown               49    137  (340)  24  
+  313   24.7  6.4  1.1  contig1   14089 14182 (30997) + rnd-5_family-288  Unknown              163    261  (216)  24  
+  524   13.0  1.0  1.0  contig1   14660 14760 (30419) + rnd-5_family-128  Unknown               92    192  (167)  25  
+  350   10.0  0.0  0.0  contig1   14801 14850 (30329) C rnd-1_family-420  Unknown             (84)     50      1  26  
+  305   18.9  2.6  3.9  contig1   15797 15873 (29306) C rnd-5_family-3538 Unknown              (2)    178    103  27  
+  536   12.4 22.8  2.3  contig1   15946 16116 (29063) + rnd-5_family-107  RC/Helitron          291    496   (99)  28  
+  329   10.4  0.0  0.0  contig1   16127 16174 (29005) + rnd-1_family-40   Unknown                1     48    (0)  29 *
+ 1758    8.6  0.8  9.2  contig1   16132 16440 (28739) + rnd-4_family-146  RC/Helitron           17    270  (974)  30  
+ 1149    9.8  9.6  2.1  contig1   16285 16472 (28707) C rnd-4_family-146  RC/Helitron          (9)   1235   1034  31 *
+  918   10.3  3.1  2.5  contig1   16445 16604 (28575) + rnd-3_family-10   DNA/TcMar-Mariner   1251   1411   (10)  32 *
+  788   20.9  9.3  1.5  contig1   16627 16830 (28349) C rnd-4_family-1925 Unknown             (36)    224      5  33  
+ 1054   12.7  6.8  4.7  contig1   16854 17099 (28080) C rnd-2_family-29   RC/Helitron        (290)    269      1  34  
+  318   14.6  0.0  0.0  contig1   17626 17680 (27499) + rnd-5_family-5175 LINE/Jockey            3     57 (1063)  35  
+  767   12.5  0.0  1.5  contig1   17799 17928 (27251) + rnd-1_family-410  LINE/Jockey            1    128    (2)  36  
+ 2149   34.5  9.2  0.2  contig1   17932 18451 (26728) + rnd-5_family-5175 LINE/Jockey          337    903  (217)  35  
+ 1172    7.4  0.0  0.0  contig1   18454 18601 (26578) + rnd-1_family-426  Unknown                1    148    (0)  37  
+  387   17.1  7.9  0.0  contig1   18684 18759 (26420) + rnd-1_family-247  LINE/Jockey          130    211   (11)  38  
+ 2237   10.4  1.2  1.2  contig1   18798 19119 (26060) + rnd-4_family-608  LINE/Jockey            3    324   (15)  39  
+  988   17.4  9.0  1.7  contig1   19717 19950 (25229) C rnd-2_family-32   RC/Helitron        (492)    251      1  40  
+  555   11.6 29.3  0.0  contig1   19883 20041 (25138) + rnd-4_family-146  RC/Helitron         1034   1239    (5)  41 *
+ 2025   12.0  8.8  0.0  contig1   20210 20551 (24628) C rnd-5_family-4539 LTR/Pao              (2)   1687   1316  42  
+  534   11.6  0.0  1.1  contig1   20548 20634 (24545) + rnd-1_family-3    RC/Helitron           24    109  (144)  43 *
+  784    6.2  0.0  0.0  contig1   20656 20752 (24427) + rnd-1_family-1    RC/Helitron            1     97   (57)  44 *
+ 2272    8.1  4.5  1.2  contig1   20752 21214 (23965) C rnd-4_family-146  RC/Helitron         (35)   1209    674  45  
+  291   20.7  0.0  0.0  contig1   21240 21297 (23882) + rnd-5_family-107  RC/Helitron          136    193  (402)  46  
+  660    6.6  1.1  0.0  contig1   21327 21417 (23762) + rnd-5_family-616  Unknown               40    131    (0)  47  
+ 1084   11.0 15.2  1.4  contig1   21420 21666 (23513) C rnd-1_family-128  Unknown             (22)    290     41  48  
+  302   10.0  0.0  0.0  contig1   21649 21688 (23491) + rnd-1_family-482  Unknown                1     40   (26)  49 *
+  373   18.0  1.2 17.8  contig1   21724 21892 (23287) + rnd-5_family-6703 LTR/Pao              617    757  (170)  50  
+ 1099    5.0  5.0  0.0  contig1   23293 23432 (21747) C rnd-1_family-120  Unknown              (0)    147      1  51  
+  342    4.5  0.0  2.2  contig1   23433 23477 (21702) C rnd-1_family-120  Unknown            (103)     44      1  52 *
+  449   10.9  0.0  0.0  contig1   23439 23502 (21677) + rnd-1_family-89   Unknown               84    147    (0)  53  
+  289   22.2  0.0  0.0  contig1   23471 23533 (21646) + rnd-1_family-73   Unknown              228    290    (0)  54 *
+ 1039    7.6  0.0  0.0  contig1   23546 23676 (21503) C rnd-1_family-73   Unknown             (13)    277    147  55  
+  341   17.2  0.0  0.0  contig1   25930 25987 (19192) + rnd-5_family-288  Unknown               78    135  (342)  56  
+ 3595   11.8  3.2  2.6  contig1   26122 26706 (18473) C rnd-5_family-2216 RC/Helitron          (3)    639     51  57  
+  285   17.4  0.0  0.0  contig1   27016 27061 (18118) + rnd-5_family-5558 Unknown              126    171  (269)  58  
+  301   12.2  0.0  5.8  contig1   27183 27234 (17945) + rnd-1_family-1    RC/Helitron            2     50  (104)  59 *
+  658   17.9  0.0  0.9  contig1   27231 27343 (17836) + rnd-4_family-146  RC/Helitron           89    200 (1044)  60  
+  310   22.4  1.2  1.2  contig1   27348 27431 (17748) + rnd-1_family-0    RC/Helitron          107    190  (270)  61  
+ 9350    2.2  3.0  0.1  contig1   27432 28732 (16447) + rnd-3_family-10   DNA/TcMar-Mariner      1   1201  (220)  62  
+  471   22.3  1.8  6.5  contig1   28734 28901 (16278) + rnd-1_family-0    RC/Helitron          241    400   (60)  61  
+ 1226    9.7  5.0  7.2  contig1   29003 29349 (15830) + rnd-1_family-1    RC/Helitron            1    317  (927)  63 *
+ 4453    9.9  0.6  0.7  contig1   29146 29828 (15351) C rnd-4_family-146  RC/Helitron        (208)   1036    355  64  
+  283   15.6  0.0  0.0  contig1   30091 30135 (15044) + rnd-4_family-108  RC/Helitron           66    110  (343)  65  
+  753   22.9 11.4  3.3  contig1   30179 30449 (14730) + rnd-5_family-2216 RC/Helitron          310    602   (40)  66  
+  367   22.4  3.6  4.5  contig1   30475 30586 (14593) + rnd-1_family-3    RC/Helitron           80    190   (63)  67  
+  315    8.2  2.0  0.0  contig1   30564 30612 (14567) + rnd-1_family-4    RC/Helitron           90    139   (57)  68 *
+  327   28.2  4.8  5.5  contig1   30861 31025 (14154) + rnd-4_family-1925 Unknown               97    260    (0)  69  
+  478   12.2 13.3  0.0  contig1   35887 35976  (9203) C rnd-5_family-2216 RC/Helitron         (14)    628    527  70  
+  465   15.6  3.1 14.2  contig1   36021 36147  (9032) C rnd-4_family-108  RC/Helitron        (307)    146     34  71  
+  297   20.6  1.4  0.0  contig1   36361 36433  (8746) + rnd-3_family-10   DNA/TcMar-Mariner   1305   1378   (43)  72  
+  285   21.0  6.2  0.0  contig1   36376 36456  (8723) + rnd-2_family-32   RC/Helitron          260    345  (398)  73 *
+  305   11.8  2.0  0.0  contig1   37138 37188  (7991) C rnd-1_family-0    RC/Helitron        (395)     65     14  74  
+  906   10.8 12.7  0.6  contig1   37201 37358  (7821) C rnd-4_family-146  RC/Helitron       (1052)    192     16  75  
+  285   11.6  0.0  0.0  contig1   37378 37420  (7759) C rnd-5_family-2216 RC/Helitron         (17)    625    583  76 *
+  795   15.9  4.8  1.1  contig1   37413 37631  (7548) C rnd-2_family-29   RC/Helitron        (306)    253      2  70  
+  807    5.7  1.9  0.0  contig1   37667 37772  (7407) C rnd-1_family-53   Unknown              (0)    112      5  77  
+  430   13.6  4.5  1.1  contig1   37848 37936  (7243) C rnd-2_family-32   RC/Helitron         (74)    669    578  78 *
+ 1235    8.6  2.1  0.5  contig1   37935 38122  (7057) + rnd-4_family-146  RC/Helitron          674    864  (380)  79  
+ 1194   16.9 24.0  0.8  contig1   38004 38361  (6818) C rnd-2_family-32   RC/Helitron        (149)    594    154  78 *
+ 1598   10.2  5.5  8.4  contig1   38362 38831  (6348) + rnd-4_family-146  RC/Helitron           43    356  (888)  80  
+ 1291    9.2  0.0  0.0  contig1   38770 38954  (6225) C rnd-2_family-32   RC/Helitron         (83)    660    476  81 *
+  693    8.0  5.3  0.9  contig1   39581 39694  (5485) + rnd-3_family-10   DNA/TcMar-Mariner   1296   1414    (7)  82 *
+ 2674   10.1  0.7  1.9  contig1   39636 40096  (5083) + rnd-4_family-146  RC/Helitron          248    763  (481)  83  
+ 1535    4.9  0.0  1.6  contig1   40095 40281  (4898) C rnd-2_family-19   RC/Helitron         (43)    184      1  84 *
+ 2609   13.1  4.0  0.4  contig1   40279 40731  (4448) C rnd-4_family-146  RC/Helitron        (235)   1009    541  85 *
+ 2729    8.5  4.0  0.2  contig1   40439 40861  (4318) + rnd-1_family-0    RC/Helitron           21    459    (1)  86  
+  349   26.1  0.8  2.5  contig1   42871 42992  (2187) + rnd-4_family-146  RC/Helitron          539    658  (586)  87  
+  318   21.6 15.9  0.0  contig1   43030 43117  (2062) C rnd-4_family-146  RC/Helitron       (1073)    171     70  85  
+  260   23.5  0.0  1.4  contig1   43192 43260  (1919) C rnd-1_family-0    RC/Helitron        (281)    179    112  88  
+  446   14.5  0.0  0.0  contig1   43299 43367  (1812) C rnd-1_family-53   Unknown              (2)    110     42  89  
+  421   21.4 12.7  0.0  contig1   43323 43448  (1731) + rnd-5_family-8111 Unknown              105    246  (156)  90 *
+  431   16.2  0.0  0.0  contig1   43482 43561  (1618) C rnd-1_family-99   Unknown             (56)     84      5  91 *
+  595   14.3  0.0  0.0  contig1   43533 43630  (1549) C rnd-1_family-50   Unknown              (0)    128     31  92  
+ 1122   16.0  6.8  0.0  contig1   43634 43839  (1340) + rnd-4_family-146  RC/Helitron           64    283  (961)  93  
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
@@ -0,0 +1,103 @@
+   SW   perc perc perc  query     position in query     matching          repeat              position in repeat
+score   div. del. ins.  sequence  begin end    (left)   repeat            class/family      begin  end    (left)  ID
+
+ 2239   13.1 11.2  0.7  contig1       7   452 (44727) C rnd-4_family-146  RC/Helitron        (320)    924    432   1  
+ 1795   13.4 12.0  1.2  contig1     224   631 (44548) + rnd-1_family-0    RC/Helitron            9    460    (0)   2 *
+  309   28.3  5.6  4.0  contig1    5522  5646 (39533) C rnd-5_family-2216 RC/Helitron        (185)    457    331   3  
+  565   19.4  1.6  1.6  contig1    6493  6618 (38561) + rnd-1_family-2    RC/Helitron            2    127   (29)   4  
+  267    9.8 13.7  0.0  contig1    6685  6735 (38444) + rnd-1_family-31   RC/Helitron            1     58    (0)   5 *
+ 2033    5.7  4.2  0.0  contig1    6702  6963 (38216) + rnd-4_family-146  RC/Helitron           44    316  (928)   6 *
+ 2466   14.1  4.2  2.8  contig1    6768  7489 (37690) C rnd-4_family-146  RC/Helitron          (0)   1244    351   7  
+  317   13.8  0.0  0.0  contig1    7498  7555 (37624) + rnd-1_family-99   Unknown               82    139    (1)   8  
+  271   10.9  0.0  0.0  contig1    7516  7561 (37618) C rnd-1_family-99   Unknown             (86)     54      9   9 *
+  639   13.4  0.0  0.0  contig1    7560  7656 (37523) + rnd-1_family-34   Unknown               92    188    (0)  10 *
+ 1471   16.2  3.0  0.0  contig1    7653  7917 (37262) C rnd-5_family-8111 Unknown            (129)    273      1  11  
+  465   22.9  3.1  6.2  contig1    8032  8252 (36927) C rnd-1_family-4    RC/Helitron          (0)    196      1  12 *
+  793    4.2  0.0  0.0  contig1    8234  8328 (36851) C rnd-1_family-7    RC/Helitron          (2)    140     46  13  
+  747   10.1  7.6  0.0  contig1    8325  8443 (36736) C rnd-1_family-2    RC/Helitron         (25)    131      4  14 *
+ 1621   12.6  5.3  2.8  contig1    8906  9259 (35920) + rnd-4_family-146  RC/Helitron           72    319  (925)  15 *
+ 2224   12.4  8.7  2.1  contig1    9105  9541 (35638) C rnd-4_family-146  RC/Helitron        (207)   1037    572  16 *
+ 2442    7.1 11.9  1.7  contig1    9294  9706 (35473) + rnd-1_family-0    RC/Helitron            6    460    (0)  17  
+  308    7.0  0.0  0.0  contig1    9954  9996 (35183) + rnd-5_family-8111 Unknown                2     44  (358)  18  
+  660   18.8  8.3  0.0  contig1   10019 10151 (35028) + rnd-5_family-8111 Unknown              186    329   (73)  19  
+ 1661   18.1  9.3  3.6  contig1   10159 10576 (34603) C rnd-4_family-306  Unknown             (78)    468     27  20  
+ 1521   12.2 14.9  1.3  contig1   10577 10891 (34288) C rnd-4_family-146  RC/Helitron        (532)    712    355  21  
+  555   10.0  0.0  0.0  contig1   10899 10978 (34201) + rnd-1_family-211  Unknown                2     81   (20)  22  
+  356   15.7 30.0  0.0  contig1   11135 11262 (33917) C rnd-4_family-146  RC/Helitron       (1085)    159      2  21  
+  307   25.5  4.2  2.1  contig1   11920 12015 (33164) C rnd-4_family-1925 Unknown              (0)    260    163  23  
+  436   23.6  0.0  1.1  contig1   13661 13750 (31429) + rnd-5_family-288  Unknown               49    137  (340)  24  
+  313   24.7  6.4  1.1  contig1   14089 14182 (30997) + rnd-5_family-288  Unknown              163    261  (216)  24  
+  524   13.0  1.0  1.0  contig1   14660 14760 (30419) + rnd-5_family-128  Unknown               92    192  (167)  25  
+  350   10.0  0.0  0.0  contig1   14801 14850 (30329) C rnd-1_family-420  Unknown             (84)     50      1  26  
+  305   18.9  2.6  3.9  contig1   15797 15873 (29306) C rnd-5_family-3538 Unknown              (2)    178    103  27  
+  536   12.4 22.8  2.3  contig1   15946 16116 (29063) + rnd-5_family-107  RC/Helitron          291    496   (99)  28  
+  329   10.4  0.0  0.0  contig1   16127 16174 (29005) + rnd-1_family-40   Unknown                1     48    (0)  29 *
+ 1758    8.6  0.8  9.2  contig1   16132 16440 (28739) + rnd-4_family-146  RC/Helitron           17    270  (974)  30  
+ 1149    9.8  9.6  2.1  contig1   16285 16472 (28707) C rnd-4_family-146  RC/Helitron          (9)   1235   1034  31 *
+  918   10.3  3.1  2.5  contig1   16445 16604 (28575) + rnd-3_family-10   DNA/TcMar-Mariner   1251   1411   (10)  32 *
+  788   20.9  9.3  1.5  contig1   16627 16830 (28349) C rnd-4_family-1925 Unknown             (36)    224      5  33  
+ 1054   12.7  6.8  4.7  contig1   16854 17099 (28080) C rnd-2_family-29   RC/Helitron        (290)    269      1  34  
+  318   14.6  0.0  0.0  contig1   17626 17680 (27499) + rnd-5_family-5175 LINE/Jockey            3     57 (1063)  35  
+  767   12.5  0.0  1.5  contig1   17799 17928 (27251) + rnd-1_family-410  LINE/Jockey            1    128    (2)  36  
+ 2149   34.5  9.2  0.2  contig1   17932 18451 (26728) + rnd-5_family-5175 LINE/Jockey          337    903  (217)  35  
+ 1172    7.4  0.0  0.0  contig1   18454 18601 (26578) + rnd-1_family-426  Unknown                1    148    (0)  37  
+  387   17.1  7.9  0.0  contig1   18684 18759 (26420) + rnd-1_family-247  LINE/Jockey          130    211   (11)  38  
+ 2237   10.4  1.2  1.2  contig1   18798 19119 (26060) + rnd-4_family-608  LINE/Jockey            3    324   (15)  39  
+  988   17.4  9.0  1.7  contig1   19717 19950 (25229) C rnd-2_family-32   RC/Helitron        (492)    251      1  40  
+  555   11.6 29.3  0.0  contig1   19883 20041 (25138) + rnd-4_family-146  RC/Helitron         1034   1239    (5)  41 *
+ 2025   12.0  8.8  0.0  contig1   20210 20551 (24628) C rnd-5_family-4539 LTR/Pao              (2)   1687   1316  42  
+  534   11.6  0.0  1.1  contig1   20548 20634 (24545) + rnd-1_family-3    RC/Helitron           24    109  (144)  43 *
+  784    6.2  0.0  0.0  contig1   20656 20752 (24427) + rnd-1_family-1    RC/Helitron            1     97   (57)  44 *
+ 2272    8.1  4.5  1.2  contig1   20752 21214 (23965) C rnd-4_family-146  RC/Helitron         (35)   1209    674  45  
+  291   20.7  0.0  0.0  contig1   21240 21297 (23882) + rnd-5_family-107  RC/Helitron          136    193  (402)  46  
+  660    6.6  1.1  0.0  contig1   21327 21417 (23762) + rnd-5_family-616  Unknown               40    131    (0)  47  
+ 1084   11.0 15.2  1.4  contig1   21420 21666 (23513) C rnd-1_family-128  Unknown             (22)    290     41  48  
+  302   10.0  0.0  0.0  contig1   21649 21688 (23491) + rnd-1_family-482  Unknown                1     40   (26)  49 *
+  373   18.0  1.2 17.8  contig1   21724 21892 (23287) + rnd-5_family-6703 LTR/Pao              617    757  (170)  50  
+ 1099    5.0  5.0  0.0  contig1   23293 23432 (21747) C rnd-1_family-120  Unknown              (0)    147      1  51  
+  342    4.5  0.0  2.2  contig1   23433 23477 (21702) C rnd-1_family-120  Unknown            (103)     44      1  52 *
+  449   10.9  0.0  0.0  contig1   23439 23502 (21677) + rnd-1_family-89   Unknown               84    147    (0)  53  
+  289   22.2  0.0  0.0  contig1   23471 23533 (21646) + rnd-1_family-73   Unknown              228    290    (0)  54 *
+ 1039    7.6  0.0  0.0  contig1   23546 23676 (21503) C rnd-1_family-73   Unknown             (13)    277    147  55  
+  341   17.2  0.0  0.0  contig1   25930 25987 (19192) + rnd-5_family-288  Unknown               78    135  (342)  56  
+ 3595   11.8  3.2  2.6  contig1   26122 26706 (18473) C rnd-5_family-2216 RC/Helitron          (3)    639     51  57  
+  285   17.4  0.0  0.0  contig1   27016 27061 (18118) + rnd-5_family-5558 Unknown              126    171  (269)  58  
+  301   12.2  0.0  5.8  contig1   27183 27234 (17945) + rnd-1_family-1    RC/Helitron            2     50  (104)  59 *
+  658   17.9  0.0  0.9  contig1   27231 27343 (17836) + rnd-4_family-146  RC/Helitron           89    200 (1044)  60  
+  310   22.4  1.2  1.2  contig1   27348 27431 (17748) + rnd-1_family-0    RC/Helitron          107    190  (270)  61  
+ 9350    2.2  3.0  0.1  contig1   27432 28732 (16447) + rnd-3_family-10   DNA/TcMar-Mariner      1   1201  (220)  62  
+  471   22.3  1.8  6.5  contig1   28734 28901 (16278) + rnd-1_family-0    RC/Helitron          241    400   (60)  61  
+ 1226    9.7  5.0  7.2  contig1   29003 29349 (15830) + rnd-1_family-1    RC/Helitron            1    317  (927)  63 *
+ 4453    9.9  0.6  0.7  contig1   29146 29828 (15351) C rnd-4_family-146  RC/Helitron        (208)   1036    355  64  
+  283   15.6  0.0  0.0  contig1   30091 30135 (15044) + rnd-4_family-108  RC/Helitron           66    110  (343)  65  
+  753   22.9 11.4  3.3  contig1   30179 30449 (14730) + rnd-5_family-2216 RC/Helitron          310    602   (40)  66  
+  367   22.4  3.6  4.5  contig1   30475 30586 (14593) + rnd-1_family-3    RC/Helitron           80    190   (63)  67  
+  315    8.2  2.0  0.0  contig1   30564 30612 (14567) + rnd-1_family-4    RC/Helitron           90    139   (57)  68 *
+  327   28.2  4.8  5.5  contig1   30861 31025 (14154) + rnd-4_family-1925 Unknown               97    260    (0)  69  
+  478   12.2 13.3  0.0  contig1   35887 35976  (9203) C rnd-5_family-2216 RC/Helitron         (14)    628    527  70  
+  465   15.6  3.1 14.2  contig1   36021 36147  (9032) C rnd-4_family-108  RC/Helitron        (307)    146     34  71  
+  297   20.6  1.4  0.0  contig1   36361 36433  (8746) + rnd-3_family-10   DNA/TcMar-Mariner   1305   1378   (43)  72  
+  285   21.0  6.2  0.0  contig1   36376 36456  (8723) + rnd-2_family-32   RC/Helitron          260    345  (398)  73 *
+  305   11.8  2.0  0.0  contig1   37138 37188  (7991) C rnd-1_family-0    RC/Helitron        (395)     65     14  74  
+  906   10.8 12.7  0.6  contig1   37201 37358  (7821) C rnd-4_family-146  RC/Helitron       (1052)    192     16  75  
+  285   11.6  0.0  0.0  contig1   37378 37420  (7759) C rnd-5_family-2216 RC/Helitron         (17)    625    583  76 *
+  795   15.9  4.8  1.1  contig1   37413 37631  (7548) C rnd-2_family-29   RC/Helitron        (306)    253      2  70  
+  807    5.7  1.9  0.0  contig1   37667 37772  (7407) C rnd-1_family-53   Unknown              (0)    112      5  77  
+  430   13.6  4.5  1.1  contig1   37848 37936  (7243) C rnd-2_family-32   RC/Helitron         (74)    669    578  78 *
+ 1235    8.6  2.1  0.5  contig1   37935 38122  (7057) + rnd-4_family-146  RC/Helitron          674    864  (380)  79  
+ 1194   16.9 24.0  0.8  contig1   38004 38361  (6818) C rnd-2_family-32   RC/Helitron        (149)    594    154  78 *
+ 1598   10.2  5.5  8.4  contig1   38362 38831  (6348) + rnd-4_family-146  RC/Helitron           43    356  (888)  80  
+ 1291    9.2  0.0  0.0  contig1   38770 38954  (6225) C rnd-2_family-32   RC/Helitron         (83)    660    476  81 *
+  693    8.0  5.3  0.9  contig1   39581 39694  (5485) + rnd-3_family-10   DNA/TcMar-Mariner   1296   1414    (7)  82 *
+ 2674   10.1  0.7  1.9  contig1   39636 40096  (5083) + rnd-4_family-146  RC/Helitron          248    763  (481)  83  
+ 1535    4.9  0.0  1.6  contig1   40095 40281  (4898) C rnd-2_family-19   RC/Helitron         (43)    184      1  84 *
+ 2609   13.1  4.0  0.4  contig1   40279 40731  (4448) C rnd-4_family-146  RC/Helitron        (235)   1009    541  85 *
+ 2729    8.5  4.0  0.2  contig1   40439 40861  (4318) + rnd-1_family-0    RC/Helitron           21    459    (1)  86  
+  349   26.1  0.8  2.5  contig1   42871 42992  (2187) + rnd-4_family-146  RC/Helitron          539    658  (586)  87  
+  318   21.6 15.9  0.0  contig1   43030 43117  (2062) C rnd-4_family-146  RC/Helitron       (1073)    171     70  85  
+  260   23.5  0.0  1.4  contig1   43192 43260  (1919) C rnd-1_family-0    RC/Helitron        (281)    179    112  88  
+  446   14.5  0.0  0.0  contig1   43299 43367  (1812) C rnd-1_family-53   Unknown              (2)    110     42  89  
+  421   21.4 12.7  0.0  contig1   43323 43448  (1731) + rnd-5_family-8111 Unknown              105    246  (156)  90 *
+  431   16.2  0.0  0.0  contig1   43482 43561  (1618) C rnd-1_family-99   Unknown             (56)     84      5  91 *
+  595   14.3  0.0  0.0  contig1   43533 43630  (1549) C rnd-1_family-50   Unknown              (0)    128     31  92  
+ 1122   16.0  6.8  0.0  contig1   43634 43839  (1340) + rnd-4_family-146  RC/Helitron           64    283  (961)  93  
diff -r 000000000000 -r fb318f9a36f3 test-data/contig1.out.2bit
Binary file test-data/contig1.out.2bit has changed
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
@@ -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>
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>
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>