# HG changeset patch # User yating-l # Date 1485987362 18000 # Node ID 70d7377d5e242da02ceeca92f434cbda31030898 # Parent fbeff1df110bc91a244d1374fa777e40861e68e8 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty diff -r fbeff1df110b -r 70d7377d5e24 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Wed Feb 01 17:16:02 2017 -0500 @@ -0,0 +1,14 @@ +Galaxy wrapper for UCSC BLAT alignment tool +=========================================== +BLAT (http://genome.ucsc.edu/goldenPath/help/blatSpec.html) is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments. + +Features +-------- +1. Perform rapid mRNA/DNA and cross-species protein alignments using blat +2. Sort the output file +3. Filter cDNA alignments in psl format using pslCDnaFilter + +Licence +------- +Please note that commercial download and installation of the Blat and In-Silico PCR software may be licensed through Kent Informatics (http://www.kentinformatics.com). + diff -r fbeff1df110b -r 70d7377d5e24 blat.xml --- a/blat.xml Tue Jan 31 18:31:42 2017 -0500 +++ b/blat.xml Wed Feb 01 17:16:02 2017 -0500 @@ -1,5 +1,6 @@ + - Rapidly align sequences to the genome + Standalone blat sequence search command line tool ucsc_tools_340_for_BLAT @@ -13,8 +14,46 @@ -mask=$mask '${database}' '${query}' - '${output}' - + output + && sort -k 10,10 -k 12,12n output > '${output_sorted}' + && pslReps -minAli=0.25 '${output_sorted}' output.reps.psl output.reps.psr + && faPolyASizes '${query}' query.polyA + #if $filter_param.filter =="yes" + && pslCDnaFilter + #if $filter_param.assembly_type == "native" + -localNearBest=0.001 + #if $filter_param.assembly_category == "finished" + -minId=0.95 + -minCover=0.25 + #else if $filter_param.assembly_category == "well-ordered" + -minId=0.95 + -minCover=0.15 + #else + -minId=0.94 + -minAlnSize=80 + #end if + #else + -localNearBest=0.010 + #if $filter_param.assembly_category == "finished" + -minId=0.35 + -minCover=0.25 + #else if $filter_param.assembly_category == "well-ordered" + -minId=0.35 + -minCover=0.15 + #else + -minId=0.33 + -minAlnSize=80 + #end if + #end if + -minQSize=20 + -ignoreIntrons + -repsAsMatch + -ignoreNs + -bestOverlap + -polyASizes=query.polyA + output.reps.psl + '${output_filtered}' + #end if ]]> @@ -40,93 +79,27 @@ - + + + + + + + + + + + + - + + @@ -136,9 +109,64 @@ - + + + + + - + + + + + + @article{kent2002blat, + title={BLAT—the BLAST-like alignment tool}, + author={Kent, W James}, + journal={Genome research}, + volume={12}, + number={4}, + pages={656--664}, + year={2002}, + publisher={Cold Spring Harbor Lab} + } + diff -r fbeff1df110b -r 70d7377d5e24 test-data/amaVit1_Gallus_gallus.psl --- a/test-data/amaVit1_Gallus_gallus.psl Tue Jan 31 18:31:42 2017 -0500 +++ b/test-data/amaVit1_Gallus_gallus.psl Wed Feb 01 17:16:02 2017 -0500 @@ -1,12 +1,12 @@ 2134 377 0 62 6 361 28 33978 ++ NM_001006176 3248 296 3230 LMAW01000001.1 10443977 10027590 10064141 29 110,48,10,76,75,152,66,51,87,83,55,56,148,96,63,24,177,107,83,145,109,83,145,90,117,129,68,93,27, 296,406,454,502,578,653,844,910,961,1048,1131,1186,1242,1390,1486,1609,1741,1918,2025,2108,2253,2362,2445,2590,2680,2797,2926,3034,3203, 10027590,10031154,10031353,10031517,10033261,10033696,10034454,10035646,10043484,10043794,10059668,10059824,10059973,10060798,10060979,10061265,10061487,10061740,10061947,10062143,10062365,10062584,10062743,10063001,10063188,10063383,10063616,10063806,10064114, +1247 370 0 44 6 280 17 96639 +- NM_001012804 4592 121 2062 LMAW01000001.1 10443977 517465 615765 18 119,32,74,112,2,87,150,114,39,171,3,94,58,142,81,107,137,139, 121,240,272,355,467,469,598,757,1066,1129,1300,1303,1397,1455,1597,1679,1786,1923, 9828212,9828431,9869264,9881475,9881600,9882641,9893172,9893708,9899022,9904744,9904997,9908755,9909749,9911745,9915154,9915481,9920844,9926373, 420 114 0 0 4 99 3 7093 ++ NM_001031013 971 69 702 LMAW01000002.1 5883884 3610886 3618513 5 33,66,21,276,138, 69,138,232,285,564, 3610886,3610955,3617941,3618099,3618375, -189 73 0 0 4 773 4 13674 ++ NM_204766 5992 553 1588 LMAW01000003.1 4188689 2559457 2573393 5 84,66,33,13,66, 553,739,844,1457,1522, 2559457,2563244,2563349,2570767,2573327, -143 58 0 19 3 659 4 9089 ++ NM_204766 5992 574 1453 LMAW01000003.1 4188689 259524 268833 5 27,80,11,66,36, 574,700,780,847,1417, 259524,261255,261529,262379,268797, -3724 1107 0 326 14 609 44 22663 ++ NM_204766 5992 49 5815 LMAW01000002.1 5883884 103604 131424 45 51,78,132,3,152,2,29,75,90,63,1,95,81,3,136,119,150,2,169,180,123,48,90,117,123,134,241,261,177,146,90,72,267,129,81,2,196,348,116,193,106,123,177,99,87, 49,154,256,388,391,543,545,574,691,781,844,845,967,1048,1051,1187,1306,1456,1458,1627,1807,1960,2008,2098,2215,2338,2472,2713,2974,3151,3298,3388,3493,3778,3943,4024,4026,4222,4696,4812,5051,5212,5335,5608,5728, 103604,104407,107764,107909,108002,108233,108257,109261,112047,112967,113036,113148,114257,114391,114866,116183,116438,116593,116908,117767,118030,118682,120119,120672,121329,122185,122724,123518,123945,124449,124904,125793,125898,126790,127405,127543,127717,128055,129238,129442,129761,130020,130254,131103,131337, -537 234 0 42 7 1113 7 34987 ++ NM_204766 5992 262 2188 LMAW01000001.1 10443977 9729332 9765132 8 108,153,66,93,39,171,99,84, 262,388,574,688,1414,1459,1981,2104, 9729332,9734141,9751019,9755220,9762042,9762555,9764665,9765048, -1247 370 0 44 6 280 17 96639 +- NM_001012804 4592 121 2062 LMAW01000001.1 10443977 517465 615765 18 119,32,74,112,2,87,150,114,39,171,3,94,58,142,81,107,137,139, 121,240,272,355,467,469,598,757,1066,1129,1300,1303,1397,1455,1597,1679,1786,1923, 9828212,9828431,9869264,9881475,9881600,9882641,9893172,9893708,9899022,9904744,9904997,9908755,9909749,9911745,9915154,9915481,9920844,9926373, 2710 404 0 198 24 2053 34 11593 +- NM_001292086 6644 10 5375 LMAW01000003.1 4188689 2820233 2835138 37 64,727,107,5,90,146,87,93,135,137,171,93,72,90,69,90,23,34,9,72,125,70,106,21,23,161,26,29,93,15,45,18,11,12,54,162,27, 10,74,801,908,913,1003,1149,1236,1329,1464,1617,1792,1885,2049,2163,2350,2918,3036,3070,3366,3445,3576,3647,3794,3985,4008,4236,4263,4476,4603,4688,4742,4882,4941,5031,5113,5348, 1353551,1355131,1356116,1356798,1356971,1357445,1359020,1359444,1359816,1360523,1360971,1361443,1365082,1365245,1365351,1365525,1366096,1366220,1366255,1366474,1366549,1366674,1366749,1366889,1367081,1367105,1367332,1367358,1367558,1367688,1367786,1367837,1367979,1368029,1368113,1368194,1368429, 200 50 0 0 0 0 1 24 +- NM_001292086 6644 481 731 LMAW01000003.1 4188689 2832850 2833124 2 110,140, 481,591, 1355565,1355699, 182 48 0 20 1 24 0 0 +- NM_001292086 6644 508 782 LMAW01000003.1 4188689 2832901 2833151 2 102,148, 508,634, 1355538,1355640, 92 25 0 0 0 0 1 183 +- NM_001292086 6644 562 679 LMAW01000003.1 4188689 2832851 2833151 2 43,74, 562,605, 1355538,1355764, 49 11 0 0 0 0 0 0 +- NM_001292086 6644 619 679 LMAW01000003.1 4188689 2833085 2833145 1 60, 619, 1355544, +3724 1107 0 326 14 609 44 22663 ++ NM_204766 5992 49 5815 LMAW01000002.1 5883884 103604 131424 45 51,78,132,3,152,2,29,75,90,63,1,95,81,3,136,119,150,2,169,180,123,48,90,117,123,134,241,261,177,146,90,72,267,129,81,2,196,348,116,193,106,123,177,99,87, 49,154,256,388,391,543,545,574,691,781,844,845,967,1048,1051,1187,1306,1456,1458,1627,1807,1960,2008,2098,2215,2338,2472,2713,2974,3151,3298,3388,3493,3778,3943,4024,4026,4222,4696,4812,5051,5212,5335,5608,5728, 103604,104407,107764,107909,108002,108233,108257,109261,112047,112967,113036,113148,114257,114391,114866,116183,116438,116593,116908,117767,118030,118682,120119,120672,121329,122185,122724,123518,123945,124449,124904,125793,125898,126790,127405,127543,127717,128055,129238,129442,129761,130020,130254,131103,131337, +537 234 0 42 7 1113 7 34987 ++ NM_204766 5992 262 2188 LMAW01000001.1 10443977 9729332 9765132 8 108,153,66,93,39,171,99,84, 262,388,574,688,1414,1459,1981,2104, 9729332,9734141,9751019,9755220,9762042,9762555,9764665,9765048, +189 73 0 0 4 773 4 13674 ++ NM_204766 5992 553 1588 LMAW01000003.1 4188689 2559457 2573393 5 84,66,33,13,66, 553,739,844,1457,1522, 2559457,2563244,2563349,2570767,2573327, +143 58 0 19 3 659 4 9089 ++ NM_204766 5992 574 1453 LMAW01000003.1 4188689 259524 268833 5 27,80,11,66,36, 574,700,780,847,1417, 259524,261255,261529,262379,268797, diff -r fbeff1df110b -r 70d7377d5e24 test-data/amaVit1_Gallus_gallus_filtered.psl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amaVit1_Gallus_gallus_filtered.psl Wed Feb 01 17:16:02 2017 -0500 @@ -0,0 +1,5 @@ +2134 377 0 62 6 361 28 33978 ++ NM_001006176 3248 296 3230 LMAW01000001.1 10443977 10027590 10064141 29 110,48,10,76,75,152,66,51,87,83,55,56,148,96,63,24,177,107,83,145,109,83,145,90,117,129,68,93,27, 296,406,454,502,578,653,844,910,961,1048,1131,1186,1242,1390,1486,1609,1741,1918,2025,2108,2253,2362,2445,2590,2680,2797,2926,3034,3203, 10027590,10031154,10031353,10031517,10033261,10033696,10034454,10035646,10043484,10043794,10059668,10059824,10059973,10060798,10060979,10061265,10061487,10061740,10061947,10062143,10062365,10062584,10062743,10063001,10063188,10063383,10063616,10063806,10064114, +1247 370 0 44 6 280 17 96639 +- NM_001012804 4592 121 2062 LMAW01000001.1 10443977 517465 615765 18 119,32,74,112,2,87,150,114,39,171,3,94,58,142,81,107,137,139, 121,240,272,355,467,469,598,757,1066,1129,1300,1303,1397,1455,1597,1679,1786,1923, 9828212,9828431,9869264,9881475,9881600,9882641,9893172,9893708,9899022,9904744,9904997,9908755,9909749,9911745,9915154,9915481,9920844,9926373, +420 114 0 0 4 99 3 7093 ++ NM_001031013 971 69 702 LMAW01000002.1 5883884 3610886 3618513 5 33,66,21,276,138, 69,138,232,285,564, 3610886,3610955,3617941,3618099,3618375, +2710 404 0 198 24 2053 34 11593 +- NM_001292086 6644 10 5375 LMAW01000003.1 4188689 2820233 2835138 37 64,727,107,5,90,146,87,93,135,137,171,93,72,90,69,90,23,34,9,72,125,70,106,21,23,161,26,29,93,15,45,18,11,12,54,162,27, 10,74,801,908,913,1003,1149,1236,1329,1464,1617,1792,1885,2049,2163,2350,2918,3036,3070,3366,3445,3576,3647,3794,3985,4008,4236,4263,4476,4603,4688,4742,4882,4941,5031,5113,5348, 1353551,1355131,1356116,1356798,1356971,1357445,1359020,1359444,1359816,1360523,1360971,1361443,1365082,1365245,1365351,1365525,1366096,1366220,1366255,1366474,1366549,1366674,1366749,1366889,1367081,1367105,1367332,1367358,1367558,1367688,1367786,1367837,1367979,1368029,1368113,1368194,1368429, +3724 1107 0 326 14 609 44 22663 ++ NM_204766 5992 49 5815 LMAW01000002.1 5883884 103604 131424 45 51,78,132,3,152,2,29,75,90,63,1,95,81,3,136,119,150,2,169,180,123,48,90,117,123,134,241,261,177,146,90,72,267,129,81,2,196,348,116,193,106,123,177,99,87, 49,154,256,388,391,543,545,574,691,781,844,845,967,1048,1051,1187,1306,1456,1458,1627,1807,1960,2008,2098,2215,2338,2472,2713,2974,3151,3298,3388,3493,3778,3943,4024,4026,4222,4696,4812,5051,5212,5335,5608,5728, 103604,104407,107764,107909,108002,108233,108257,109261,112047,112967,113036,113148,114257,114391,114866,116183,116438,116593,116908,117767,118030,118682,120119,120672,121329,122185,122724,123518,123945,124449,124904,125793,125898,126790,127405,127543,127717,128055,129238,129442,129761,130020,130254,131103,131337, diff -r fbeff1df110b -r 70d7377d5e24 tool_dependencies.xml --- a/tool_dependencies.xml Tue Jan 31 18:31:42 2017 -0500 +++ b/tool_dependencies.xml Wed Feb 01 17:16:02 2017 -0500 @@ -1,8 +1,11 @@ -