details: http://www.bx.psu.edu/hg/galaxy/rev/1cf9480dd090 changeset: 2746:1cf9480dd090 user: Kelly Vincent <kpvincent@bx.psu.edu> date: Tue Sep 22 10:09:23 2009 -0400 description: Modified Concatenate queries tool to have two base files to concatenate and the option to add a third or more. Also removed to unnecessary sort1 test files. 5 file(s) affected in this change: test-data/cat_wrapper_out1.bed test-data/sort1_alpha.bed test-data/sort1_num.bed tools/filters/catWrapper.py tools/filters/catWrapper.xml diffs (226 lines): diff -r e9104d403af7 -r 1cf9480dd090 test-data/cat_wrapper_out1.bed --- a/test-data/cat_wrapper_out1.bed Tue Sep 22 08:59:36 2009 -0400 +++ b/test-data/cat_wrapper_out1.bed Tue Sep 22 10:09:23 2009 -0400 @@ -131,3 +131,28 @@ chrX 152648964 152649196 NM_000425_cds_0_0_chrX_152648965_r 0 - chrX 152691446 152691471 AF101728_cds_0_0_chrX_152691447_f 0 + chrX 152694029 152694263 BC052303_cds_0_0_chrX_152694030_r 0 - +chr1 147962006 147975713 NM_005997 0 - 147962192 147975670 0 6 574,145,177,115,153,160, 0,1543,7859,9048,9340,13547, +chr1 147984101 148035079 BC007833 0 + 147984545 148033414 0 14 529,32,81,131,118,153,300,206,84,49,85,130,46,1668, 0,25695,28767,33118,33695,33998,35644,38005,39629,40577,41402,43885,48367,49310, +chr1 148077485 148111797 NM_002651 0 - 148078400 148111728 0 12 1097,121,133,266,124,105,110,228,228,45,937,77, 0,2081,2472,6871,9907,10257,11604,14199,15637,18274,23636,34235, +chr1 148185113 148187485 NM_002796 0 + 148185136 148187378 0 7 163,207,147,82,117,89,120, 0,416,877,1199,1674,1977,2252, +chr2 118288484 118306183 NM_006773 0 + 118288583 118304530 0 14 184,285,144,136,101,200,115,140,162,153,114,57,178,1796, 0,2765,4970,6482,6971,7183,7468,9890,10261,10768,11590,14270,14610,15903, +chr2 118389378 118390700 BC005078 0 - 118390395 118390500 0 1 1322, 0, +chr2 220108603 220116964 NM_001927 0 + 220108689 220116217 0 9 664,61,96,162,126,221,44,83,789, 0,1718,1874,2118,2451,2963,5400,7286,7572, +chr2 220229182 220233943 NM_024536 0 - 220229609 220233765 0 4 1687,180,574,492, 0,1990,2660,4269, +chr5 131170738 131357870 AF099740 0 - 131311206 131357817 0 31 112,124,120,81,65,40,120,129,61,88,94,79,72,102,144,117,89,73,96,135,135,78,74,52,33,179,100,102,65,115,248, 0,11593,44117,47607,104668,109739,114675,126366,135488,137518,138009,140437,152389,153373,155388,159269,160793,162981,164403,165577,166119,167611,169501,178260,179675,180901,181658,182260,182953,183706,186884, +chr5 131424245 131426795 NM_000588 0 + 131424298 131426383 0 5 215,42,90,42,535, 0,313,1658,1872,2015, +chr5 131556201 131590458 NM_004199 0 - 131556601 131582218 0 15 471,97,69,66,54,100,71,177,194,240,138,152,97,100,170, 0,2316,2802,5596,6269,11138,11472,15098,16528,17674,21306,24587,25142,25935,34087, +chr5 131621285 131637046 NM_003687 0 + 131621326 131635821 0 7 134,152,82,179,164,118,1430, 0,4915,8770,13221,13609,14097,14331, +chr6 108298214 108386086 NM_007214 0 - 108299600 108385906 0 21 1530,105,99,102,159,174,60,83,148,155,93,133,95,109,51,59,62,113,115,100,304, 0,2490,6246,10831,12670,23164,23520,27331,31052,32526,34311,36130,36365,38609,41028,42398,43048,51479,54500,59097,87568, +chr6 108593954 108616704 NM_003269 0 + 108594662 108615360 0 9 733,146,88,236,147,97,150,106,1507, 0,5400,8778,10445,12037,14265,14749,15488,21243, +chr6 108639410 108689143 NM_152827 0 - 108640045 108688818 0 3 741,125,487, 0,2984,49246, +chr6 108722790 108950942 NM_145315 0 + 108722976 108950321 0 13 325,224,52,102,131,100,59,83,71,101,141,114,750, 0,28931,52094,60760,61796,71339,107102,152319,181970,182297,215317,224802,227402, +chr7 113320332 113924911 AK131266 0 + 113862563 113893433 0 20 285,91,178,90,58,75,138,51,201,178,214,105,88,84,77,102,122,70,164,1124, 0,201692,340175,448290,451999,484480,542213,543265,543478,545201,556083,558358,565876,567599,573029,573245,575738,577123,577946,603455, +chr7 116511232 116557294 NM_003391 0 - 116512159 116556994 0 5 1157,265,278,227,383, 0,20384,37843,43339,45679, +chr7 116713967 116902666 NM_000492 0 + 116714099 116901113 0 27 185,111,109,216,90,164,126,247,93,183,192,95,87,724,129,38,251,80,151,228,101,249,156,90,173,106,1754, 0,24290,29071,50936,54313,55285,56585,60137,62053,68678,79501,107776,110390,111971,114967,122863,123569,126711,130556,131618,134650,147559,162475,172879,184725,185496,186945, +chr7 116944658 117107512 AF377960 0 - 116945541 116979926 0 23 1129,102,133,64,186,206,179,188,153,100,87,80,96,276,118,255,151,100,204,1654,225,108,173, 0,7364,8850,10413,13893,14398,17435,24259,24615,35177,35359,45901,47221,49781,56405,66857,69787,72208,73597,80474,100111,150555,162681, +chr8 118880786 119193239 NM_000127 0 - 118881131 119192466 0 11 531,172,161,90,96,119,133,120,108,94,1735, 0,5355,7850,13505,19068,20309,23098,30863,36077,37741,310718, +chr9 128763240 128783870 NM_174933 0 + 128764156 128783586 0 12 261,118,74,159,76,48,56,63,129,117,127,370, 0,522,875,5630,12374,12603,15040,15175,18961,19191,20037,20260, +chr9 128787362 128789566 NM_014908 0 - 128787519 128789136 0 1 2204, 0, +chr9 128789530 128848928 NM_015354 0 + 128789552 128848511 0 44 54,55,74,85,81,45,93,120,212,115,201,90,66,120,127,153,127,88,77,115,121,67,129,140,107,207,170,70,68,196,78,86,146,182,201,93,159,138,75,228,132,74,130,594, 0,1491,5075,8652,9254,10312,11104,11317,20808,21702,23060,25462,31564,32908,33566,34851,35204,35595,35776,37202,38860,39111,39891,40349,42422,45499,45827,46675,47158,47621,50453,50840,51474,51926,53831,54186,55119,55619,57449,57605,57947,58352,58541,58804, +chr9 128849867 128870133 NM_020145 0 - 128850516 128869987 0 11 757,241,101,90,24,63,93,134,129,142,209, 0,1071,1736,2085,2635,4201,6376,6736,13056,14247,20057, diff -r e9104d403af7 -r 1cf9480dd090 test-data/sort1_alpha.bed --- a/test-data/sort1_alpha.bed Tue Sep 22 08:59:36 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,29 +0,0 @@ -chr1 147962006 147975713 NM_005997 0 - 147962192 147975670 0 6 574,145,177,115,153,160, 0,1543,7859,9048,9340,13547, -chr1 147984101 148035079 BC007833 0 + 147984545 148033414 0 14 529,32,81,131,118,153,300,206,84,49,85,130,46,1668, 0,25695,28767,33118,33695,33998,35644,38005,39629,40577,41402,43885,48367,49310, -chr1 148077485 148111797 NM_002651 0 - 148078400 148111728 0 12 1097,121,133,266,124,105,110,228,228,45,937,77, 0,2081,2472,6871,9907,10257,11604,14199,15637,18274,23636,34235, -chr1 148185113 148187485 NM_002796 0 + 148185136 148187378 0 7 163,207,147,82,117,89,120, 0,416,877,1199,1674,1977,2252, -chr2 118288484 118306183 NM_006773 0 + 118288583 118304530 0 14 184,285,144,136,101,200,115,140,162,153,114,57,178,1796, 0,2765,4970,6482,6971,7183,7468,9890,10261,10768,11590,14270,14610,15903, -chr2 118389378 118390700 BC005078 0 - 118390395 118390500 0 1 1322, 0, -chr2 220108603 220116964 NM_001927 0 + 220108689 220116217 0 9 664,61,96,162,126,221,44,83,789, 0,1718,1874,2118,2451,2963,5400,7286,7572, -chr2 220229182 220233943 NM_024536 0 - 220229609 220233765 0 4 1687,180,574,492, 0,1990,2660,4269, -chr5 131170738 131357870 AF099740 0 - 131311206 131357817 0 31 112,124,120,81,65,40,120,129,61,88,94,79,72,102,144,117,89,73,96,135,135,78,74,52,33,179,100,102,65,115,248, 0,11593,44117,47607,104668,109739,114675,126366,135488,137518,138009,140437,152389,153373,155388,159269,160793,162981,164403,165577,166119,167611,169501,178260,179675,180901,181658,182260,182953,183706,186884, -chr5 131424245 131426795 NM_000588 0 + 131424298 131426383 0 5 215,42,90,42,535, 0,313,1658,1872,2015, -chr5 131556201 131590458 NM_004199 0 - 131556601 131582218 0 15 471,97,69,66,54,100,71,177,194,240,138,152,97,100,170, 0,2316,2802,5596,6269,11138,11472,15098,16528,17674,21306,24587,25142,25935,34087, -chr5 131621285 131637046 NM_003687 0 + 131621326 131635821 0 7 134,152,82,179,164,118,1430, 0,4915,8770,13221,13609,14097,14331, -chr6 108298214 108386086 NM_007214 0 - 108299600 108385906 0 21 1530,105,99,102,159,174,60,83,148,155,93,133,95,109,51,59,62,113,115,100,304, 0,2490,6246,10831,12670,23164,23520,27331,31052,32526,34311,36130,36365,38609,41028,42398,43048,51479,54500,59097,87568, -chr6 108593954 108616704 NM_003269 0 + 108594662 108615360 0 9 733,146,88,236,147,97,150,106,1507, 0,5400,8778,10445,12037,14265,14749,15488,21243, -chr6 108639410 108689143 NM_152827 0 - 108640045 108688818 0 3 741,125,487, 0,2984,49246, -chr6 108722790 108950942 NM_145315 0 + 108722976 108950321 0 13 325,224,52,102,131,100,59,83,71,101,141,114,750, 0,28931,52094,60760,61796,71339,107102,152319,181970,182297,215317,224802,227402, -chr7 113320332 113924911 AK131266 0 + 113862563 113893433 0 20 285,91,178,90,58,75,138,51,201,178,214,105,88,84,77,102,122,70,164,1124, 0,201692,340175,448290,451999,484480,542213,543265,543478,545201,556083,558358,565876,567599,573029,573245,575738,577123,577946,603455, -chr7 116511232 116557294 NM_003391 0 - 116512159 116556994 0 5 1157,265,278,227,383, 0,20384,37843,43339,45679, -chr7 116713967 116902666 NM_000492 0 + 116714099 116901113 0 27 185,111,109,216,90,164,126,247,93,183,192,95,87,724,129,38,251,80,151,228,101,249,156,90,173,106,1754, 0,24290,29071,50936,54313,55285,56585,60137,62053,68678,79501,107776,110390,111971,114967,122863,123569,126711,130556,131618,134650,147559,162475,172879,184725,185496,186945, -chr7 116944658 117107512 AF377960 0 - 116945541 116979926 0 23 1129,102,133,64,186,206,179,188,153,100,87,80,96,276,118,255,151,100,204,1654,225,108,173, 0,7364,8850,10413,13893,14398,17435,24259,24615,35177,35359,45901,47221,49781,56405,66857,69787,72208,73597,80474,100111,150555,162681, -chr8 118880786 119193239 NM_000127 0 - 118881131 119192466 0 11 531,172,161,90,96,119,133,120,108,94,1735, 0,5355,7850,13505,19068,20309,23098,30863,36077,37741,310718, -chr9 128763240 128783870 NM_174933 0 + 128764156 128783586 0 12 261,118,74,159,76,48,56,63,129,117,127,370, 0,522,875,5630,12374,12603,15040,15175,18961,19191,20037,20260, -chr9 128787362 128789566 NM_014908 0 - 128787519 128789136 0 1 2204, 0, -chr9 128789530 128848928 NM_015354 0 + 128789552 128848511 0 44 54,55,74,85,81,45,93,120,212,115,201,90,66,120,127,153,127,88,77,115,121,67,129,140,107,207,170,70,68,196,78,86,146,182,201,93,159,138,75,228,132,74,130,594, 0,1491,5075,8652,9254,10312,11104,11317,20808,21702,23060,25462,31564,32908,33566,34851,35204,35595,35776,37202,38860,39111,39891,40349,42422,45499,45827,46675,47158,47621,50453,50840,51474,51926,53831,54186,55119,55619,57449,57605,57947,58352,58541,58804, -chr9 128849867 128870133 NM_020145 0 - 128850516 128869987 0 11 757,241,101,90,24,63,93,134,129,142,209, 0,1071,1736,2085,2635,4201,6376,6736,13056,14247,20057, -chrX 122719582 122773357 NM_001167 0 + 122745047 122766566 0 7 96,909,100,79,43,201,6985, 0,25433,28421,31040,32533,40295,46790, -chrX 152648233 152662158 NM_000425 0 - 152648964 152662138 0 28 963,12,73,135,156,120,174,123,202,116,223,71,198,111,125,157,167,112,144,132,185,112,171,123,203,106,11,100, 0,1436,1545,1951,2390,2653,2889,3156,3367,3772,4717,5122,5424,5868,6066,6370,6629,6909,7588,7871,8124,8456,8858,9125,10220,10660,11296,13825, -chrX 152691216 152693487 NM_000054 0 + 152691446 152693029 0 3 255,885,664, 0,616,1607, -chrX 152693677 152712545 NM_001666 0 - 152694029 152712503 0 22 586,100,93,184,74,234,106,135,78,61,103,28,85,192,102,222,129,183,63,163,205,109, 0,1693,2066,2364,2635,2794,3129,3323,3545,3752,5323,5647,5841,6032,6401,11455,11778,13249,13719,13987,14227,18759, diff -r e9104d403af7 -r 1cf9480dd090 test-data/sort1_num.bed --- a/test-data/sort1_num.bed Tue Sep 22 08:59:36 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,65 +0,0 @@ -chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - -chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + -chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - -chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + -chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - -chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - -chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + -chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - -chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + -chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - -chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + -chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - -chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - -chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + -chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - -chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + -chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + -chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - -chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + -chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - -chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - -chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + -chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - -chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + -chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + -chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - -chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + -chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - -chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + -chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - -chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + -chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - -chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - -chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + -chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - -chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + -chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + -chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - -chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + -chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - -chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + -chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - -chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + -chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - -chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + -chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - -chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + -chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - -chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - -chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + -chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - -chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + -chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + -chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - -chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + -chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - -chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - -chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + -chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - -chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + -chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - -chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + -chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - -chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + -chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - diff -r e9104d403af7 -r 1cf9480dd090 tools/filters/catWrapper.py --- a/tools/filters/catWrapper.py Tue Sep 22 08:59:36 2009 -0400 +++ b/tools/filters/catWrapper.py Tue Sep 22 10:09:23 2009 -0400 @@ -11,29 +11,19 @@ def main(): outfile = sys.argv[1] infile = sys.argv[2] - + catfiles = sys.argv[3:] try: fout = open(sys.argv[1],'w') - except: - stop_err("Output file cannot be opened for writing.") - + except Exxception, ex: + stop_err("Output file cannot be opened for writing\n" + str(ex)) try: fin = open(sys.argv[2],'r') - except: - stop_err("Input file cannot be opened for reading.") - - if len(sys.argv) < 4: - os.system("cp %s %s" %(infile,outfile)) - sys.exit() - - cmdline = "cat %s " %(infile) - for inp in sys.argv[3:]: - cmdline = cmdline + inp + " " - cmdline = cmdline + ">" + outfile + except Exception, ex: + stop_err("Input file cannot be opened for reading\n" + str(ex)) + cmdline = "cat %s %s > %s" % (infile, ' '.join(catfiles), outfile) try: os.system(cmdline) - except: - stop_err("Error encountered with cat.") + except Exception, ex: + stop_err("Error encountered with cat\n" + str(ex)) -if __name__ == "__main__": - main() \ No newline at end of file +if __name__ == "__main__": main() \ No newline at end of file diff -r e9104d403af7 -r 1cf9480dd090 tools/filters/catWrapper.xml --- a/tools/filters/catWrapper.xml Tue Sep 22 08:59:36 2009 -0400 +++ b/tools/filters/catWrapper.xml Tue Sep 22 10:09:23 2009 -0400 @@ -1,17 +1,19 @@ -<tool id="cat1" name="Concatenate queries"> +<tool id="cat1" name="Concatenate queries" version="1.0.1"> <description>tail-to-head</description> <command interpreter="python"> catWrapper.py $out_file1 - $input1 + $input1 + $input2 #for $q in $queries - ${q.input2} + ${q.input3} #end for </command> <inputs> - <param name="input1" type="data" label="Concatenate Query"/> - <repeat name="queries" title="Query"> - <param name="input2" type="data" label="Select" /> + <param name="input1" type="data" label="First query to concatenate:"/> + <param name="input2" type="data" label="Second query to concatenate:"/> + <repeat name="queries" title="Additional query"> + <param name="input3" type="data" label="Select" /> </repeat> </inputs> <outputs> @@ -21,14 +23,16 @@ <test> <param name="input1" value="1.bed"/> <param name="input2" value="2.bed"/> + <param name="input3" value="3.bed"/> <output name="out_file1" file="cat_wrapper_out1.bed"/> </test> <!--TODO: if possible, enhance the underlying test code to handle this test - the problem is multiple params with the same name "input2" + the problem is multiple params with the same name "input3" <test> <param name="input1" value="1.bed"/> <param name="input2" value="2.bed"/> - <param name="input2" value="3.bed"/> + <param name="input3" value="3.bed"/> + <param name="input3" value="4.bed"/> <output name="out_file1" file="cat_wrapper_out2.bed"/> </test> -->