| Previous changeset 33:43803843920b (2018-07-09) Next changeset 35:87644259e668 (2024-09-28) |
|
Commit message:
planemo upload commit c5f669e334bf65c1158855bd1eef88df78a8028c |
|
modified:
README.rst blat.xml test-data/all_fasta.loc test-data/amaVit1_Gallus/Gallus_gallus_RefSeq.fa test-data/amaVit1_Gallus/amaVit1.fa test-data/amaVit1_Gallus/amaVit1_Gallus_gallus.psl test-data/amaVit1_Gallus/amaVit1_Gallus_gallus_filtered.psl test-data/dbia3/dbia3.fa test-data/dbia3/dbia3.sorted.psl test-data/dbia3/dbia3_RM.out test-data/dbia3/dbia3_masked.2bit test-data/dbia3/dbia3_masked.sorted.psl test-data/dbia3/dmel-transcript.fa tool-data/all_fasta.loc.sample tool_data_table_conf.xml.sample |
|
added:
test-data/amaVit1_Gallus/amaVit1_Gallus_gallus_sorted.psl |
|
removed:
datatypes_conf.xml tool_dependencies.xml |
| b |
| diff -r 43803843920b -r 53cf9d25ef39 blat.xml --- a/blat.xml Mon Jul 09 16:31:18 2018 -0400 +++ b/blat.xml Mon Nov 21 11:11:06 2022 +0000 |
| [ |
| b'@@ -1,131 +1,195 @@\n-<?xml version="1.0"?>\n-<tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="1.1">\n- <description>Standalone blat sequence search command line tool</description>\n+<tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n+ <description>BLAST-like sequence alignment tool</description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">377</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ </macros>\n+ <xrefs>\n+ <xref type="bio.tools">blat</xref>\n+ </xrefs>\n <requirements>\n- <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">ucsc-blat</requirement>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[\n- #if str($reference_source.reference_source_selector) == "history":\n- #set $reference_fasta_filename = "localref.fa" \n- ln -s \'${reference_source.database}\' \'${reference_fasta_filename}\' &&\n- #else:\n- #set $reference_fasta_filename = str($reference_source.database.fields.path)\n- #end if\n- blat \n- #if $noHead == "yes"\n- -noHead\n- #end if\n- -q=$query_type\n- -t=$database_type\n- #if $mask_type.mask == "file.out":\n- -mask=$mask_type.mask_file\n- #else:\n- -mask=$mask_type.mask\n- #end if\n- \'$reference_fasta_filename\'\n- \'${query}\'\n- output\n- && sort -k 10,10 -k 12,12n output > \'${output_sorted}\'\n-]]></command>\n- <inputs>\n- <conditional name="reference_source">\n- <param name="reference_source_selector" type="select" label="Choose the source for the database">\n- <option value="cached">Locally cached</option>\n- <option value="history">History</option>\n- </param>\n- <when value="cached">\n- <param name="database" type="select" label="Select database">\n- <options from_data_table="all_fasta">\n- <filter type="sort_by" column="2" />\n- </options>\n- <validator type="no_options" message="A built-in database is not available" />\n- </param>\n- </when>\n- <when value="history">\n- <param name="database" type="data" format="fasta,twobit" label="Using database file, either a .fa, .nib or .2bit file" />\n- </when>\n- </conditional>\n- <param type="data" name="query" format="fasta,twobit" label="Query data, either a .fa, .nib or .2bit file"/>\n- <param type="select" name="database_type" format="text" multiple="false" label="database type" help="Choose your database type, the default is dnax" argument="-t">\n- <option value="dna">dna - DNA sequence</option>\n- <option value="prot">prot - protein sequence</option>\n- <option value="dnax" selected="true">dnax - DNA sequence translated in six frames to protein</option>\n+ #if str($reference_source.reference_source_selector) == "history":\n+ ## blat depends on file extension\n+ #if $reference_source.database.is_of_type("fasta"):\n+ #set $reference_fasta_filename = "localref.fa"\n+ #elif $reference_source.database.is_of_type("twobit"):\n+ #set $reference_fasta_filename = "localref.2bit"\n+ #else\n+ #set $reference_fasta_filename = "localref"\n+ #end if\n+ ln -s \'$reference_source.database\' \'$reference_fasta_filename\' &&\n+ #else:\n+ #set $reference_fasta_filename = str($reference_source.database.fields.path)\n+ #end if\n+\n+ blat\n+ -q=$query_type\n+ -t=$database_type\n+ $'..b'some -->\n- <test>\n+ <param name="out" value="psl -noHead" />\n+ <output name="output" value="amaVit1_Gallus/amaVit1_Gallus_gallus_sorted.psl" sort="true"/>\n+ </test>\n+ <!-- test on query of partial mRNA of Drosophila melanogaster and the database of Drosophila biamipes dot chromosome -->\n+ <test>\n <param name="reference_source_selector" value="history" />\n <param name="database" value="dbia3/dbia3.fa" />\n <param name="query" value="dbia3/dmel-transcript.fa" />\n- <param name="database_type" value="dnax" /> \n- <param name="query_type" value="rnax" /> \n- <param name="noHead" value="yes" />\n+ <param name="database_type" value="dnax" />\n+ <param name="query_type" value="rnax" />\n <param name="mask" value="lower" />\n- <output name="output_sorted" value="dbia3/dbia3.sorted.psl" />\n- </test>\n- <!-- test on the database masked by repeat masker -->\n- <test>\n+ <param name="out" value="psl -noHead" />\n+ <param name="maxIntron" value="" />\n+ <output name="output" value="dbia3/dbia3.sorted.psl" sort="true"/>\n+ </test>\n+ <!-- test on the database masked by repeat masker -->\n+ <test>\n <param name="reference_source_selector" value="history" />\n <param name="database" value="dbia3/dbia3_masked.2bit" />\n <param name="query" value="dbia3/dmel-transcript.fa" />\n- <param name="database_type" value="dnax" /> \n- <param name="query_type" value="rnax" /> \n- <param name="noHead" value="yes" />\n+ <param name="database_type" value="dnax" />\n+ <param name="query_type" value="rnax" />\n+ <param name="oneOff" value="false" />\n+ <param name="minScore" value="30" />\n+ <param name="maxGap" value="2" />\n+ <param name="trimT" value="false" />\n+ <param name="noTrimA" value="false" />\n+ <param name="fine" value="false" />\n+ <param name="maxIntron" value="750000" />\n+ <param name="extendThroughN" value="false" />\n <param name="mask" value="file.out" />\n <param name="mask_file" value="dbia3/dbia3_RM.out" />\n- <output name="output_sorted" value="dbia3/dbia3_masked.sorted.psl" />\n- </test>\n-\n- </tests> \n- <help>\n+ <param name="out" value="psl -noHead" />\n+ <output name="output" value="dbia3/dbia3_masked.sorted.psl"/>\n+ </test>\n+ </tests>\n+ <help>\n <![CDATA[\n BLAT\n ====\n-BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments. \n+BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments.\n \n-blat (version: v340)- Standalone blat sequence search command line tool. \n+blat (version: v36)- Standalone blat sequence search command line tool.\n -------------------------------------------------------------------------\n \n usage:\n@@ -139,25 +203,20 @@\n -ooc=11.ooc tells the program to load over-occurring 11-mers from\n an external file. This will increase the speed\n by a factor of 40 in many cases, but is not required.\n- output.psl is the name of the output file. \n+ output.psl is the name of the output file.\n \n documentation:\n ++++++++++++++\n \n-See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html) \n+See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html)\n \n Source code:\n ++++++++++++\n \n http://hgdownload.cse.ucsc.edu/admin/exe/\n \n-]]></help> \n-<citations>\n- <citation type="doi">10.1101/gr.229202</citation>\n-</citations> \n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1101/gr.229202</citation>\n+ </citations>\n </tool>\n- \n- \n-\n- \n- \n\\ No newline at end of file\n' |
| b |
| diff -r 43803843920b -r 53cf9d25ef39 datatypes_conf.xml --- a/datatypes_conf.xml Mon Jul 09 16:31:18 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<datatypes> - <registration> - <datatype extension="psl" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True" /> - </registration> -</datatypes> \ No newline at end of file |
| b |
| diff -r 43803843920b -r 53cf9d25ef39 test-data/amaVit1_Gallus/amaVit1_Gallus_gallus_sorted.psl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amaVit1_Gallus/amaVit1_Gallus_gallus_sorted.psl Mon Nov 21 11:11:06 2022 +0000 |
| b |
| @@ -0,0 +1,12 @@ +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, +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, +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, +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, +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, +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, +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, +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, +49 11 0 0 0 0 0 0 +- NM_001292086 6644 619 679 LMAW01000003.1 4188689 2833085 2833145 1 60, 619, 1355544, +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, +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, |
| b |
| diff -r 43803843920b -r 53cf9d25ef39 test-data/dbia3/dbia3.sorted.psl --- a/test-data/dbia3/dbia3.sorted.psl Mon Jul 09 16:31:18 2018 -0400 +++ b/test-data/dbia3/dbia3.sorted.psl Mon Nov 21 11:11:06 2022 +0000 |
| b |
| b'@@ -1,147 +1,147 @@\n 46\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0070000\t3537\t2966\t3020\tcontig55\t40015\t26192\t26246\t1\t54,\t2966,\t26192,\n-50\t10\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1826\t1886\tcontig67\t44531\t31857\t31917\t1\t60,\t1826,\t12614,\n-38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig10\t43013\t28990\t29035\t1\t45,\t1838,\t13978,\n-38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig11\t35013\t7985\t8030\t1\t45,\t1838,\t26983,\n-38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig23\t50012\t49307\t49352\t1\t45,\t1838,\t660,\n-38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig24\t40010\t29304\t29349\t1\t45,\t1838,\t10661,\n-38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig25\t75023\t20928\t20973\t1\t45,\t1838,\t54050,\n-38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig30\t70018\t55814\t55859\t1\t45,\t1838,\t14159,\n-38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig31\t40012\t15807\t15852\t1\t45,\t1838,\t24160,\n-38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig35\t48011\t33007\t33052\t1\t45,\t1838,\t14959,\n-38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig36\t45010\t8000\t8045\t1\t45,\t1838,\t36965,\n-38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig50\t40009\t19266\t19311\t1\t45,\t1838,\t20698,\n-38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig51\t50015\t4265\t4310\t1\t45,\t1838,\t45705,\n-39\t9\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig12\t56019\t44985\t45033\t1\t48,\t1838,\t44985,\n-39\t9\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig13\t45015\t38726\t38774\t1\t48,\t1838,\t6241,\n-39\t9\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig14\t45010\t23718\t23766\t1\t48,\t1838,\t21244,\n-39\t9\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig25\t75023\t51622\t51670\t1\t48,\t1838,\t51622,\n-39\t9\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig26\t40013\t1607\t1655\t1\t48,\t1838,\t1607,\n-39\t9\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig30\t70018\t36129\t36177\t1\t48,\t1838,\t36129,\n-39\t9\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig32\t40014\t25955\t26003\t1\t48,\t1838,\t14011,\n-39\t9\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig33\t40016\t10953\t11001\t1\t48,\t1838,\t29015,\n-39\t9\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig3\t40006\t37781\t37829\t1\t48,\t1838,\t2177,\n-39\t9\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig40\t60015\t52947\t52995\t1\t48,\t1838,\t52947,\n+46\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0307554\t3546\t2975\t3029\tcontig55\t40015\t26192\t26246\t1\t54,\t2975,\t26192,\n+46\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0307555\t4528\t3113\t3167\tcontig55\t40015\t26192\t26246\t1\t54,\t3113,\t26192,\n+39\t9\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig65\t45013\t12112\t12160\t1\t48,\t1838,\t12112,\n+39\t9\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig64\t40016\t32121\t32169\t1\t48,\t1838,\t32121,\n+39\t9\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig63\t55021\t47126\t47174\t1\t48,\t1838,\t47126,\n+40\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig60\t50013\t43000\t43048\t1\t48,\t1838,\t43000,\n+41\t7\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig54\t35008\t8386\t8434\t1\t48,\t1838,\t8386,\n+41\t7\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig54\t35008\t7523\t7571\t1\t48,\t1838,\t7523,\n+41\t7\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig54\t35008\t1858\t1906\t1\t48,\t1838,\t1858,\n+40\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig54\t35008\t29934\t29982\t1\t48,\t1838,\t29934,\n+41\t7\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig53\t50013\t28391\t28439\t1\t48,\t1838,\t28391,\n+41\t7\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig53\t50013\t27528\t27576\t1\t48,\t1838,\t27528,\n+41\t7\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig53\t50013\t21863\t21911\t1\t48,\t1838,\t21863,\n+41\t7\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig53\t50013\t5360\t5408\t1\t48,\t1838,\t5360,\n+40\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig53\t50013\t49939\t49987\t1\t48,\t1838,\t49939,\n+41\t7\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig52\t40012\t25367\t25415\t1\t48,\t1838,\t25367,\n+40\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig52\t40012\t1146\t1194\t1\t48,\t1838,\t1146,\n+40\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig51\t50015\t31154\t31202\t1\t48,\t1838,\t31154,\n+40\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig50\t40009\t30606\t30654\t1\t48,\t1838,\t30606,\n+41\t7\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig46\t50'..b'30\t1838\t1886\tcontig46\t50012\t31347\t31395\t1\t48,\t1838,\t18617,\n+41\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig41\t60014\t24166\t24214\t1\t48,\t1838,\t35800,\n+41\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig40\t60015\t54175\t54223\t1\t48,\t1838,\t5792,\n+39\t9\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig4\t55011\t27779\t27827\t1\t48,\t1838,\t27184,\n+38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig36\t45010\t8000\t8045\t1\t45,\t1838,\t36965,\n+38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig35\t48011\t33007\t33052\t1\t45,\t1838,\t14959,\n+39\t9\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig33\t40016\t10953\t11001\t1\t48,\t1838,\t29015,\n+39\t9\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig32\t40014\t25955\t26003\t1\t48,\t1838,\t14011,\n+38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig31\t40012\t15807\t15852\t1\t45,\t1838,\t24160,\n+38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig30\t70018\t55814\t55859\t1\t45,\t1838,\t14159,\n+39\t9\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig3\t40006\t37781\t37829\t1\t48,\t1838,\t2177,\n+40\t8\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig25\t75023\t42521\t42569\t1\t48,\t1838,\t32454,\n+38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig25\t75023\t20928\t20973\t1\t45,\t1838,\t54050,\n+38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig24\t40010\t29304\t29349\t1\t45,\t1838,\t10661,\n+38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig23\t50012\t49307\t49352\t1\t45,\t1838,\t660,\n+41\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig2\t45017\t14607\t14655\t1\t48,\t1838,\t30362,\n+41\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig15\t50014\t19711\t19759\t1\t48,\t1838,\t30255,\n+39\t9\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig14\t45010\t23718\t23766\t1\t48,\t1838,\t21244,\n+39\t9\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig13\t45015\t38726\t38774\t1\t48,\t1838,\t6241,\n+38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig11\t35013\t7985\t8030\t1\t45,\t1838,\t26983,\n+38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig10\t43013\t28990\t29035\t1\t45,\t1838,\t13978,\n+41\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig1\t45179\t29774\t29822\t1\t48,\t1838,\t15357,\n+69\t18\t0\t0\t1\t202\t1\t20788\t+-\tFBtr0300326\t4823\t2540\t2829\tcontig64\t40016\t8089\t28964\t2\t33,54,\t2540,2775,\t11052,31873,\n+69\t18\t0\t0\t1\t202\t1\t20788\t+-\tFBtr0300326\t4823\t2540\t2829\tcontig63\t55021\t23094\t43969\t2\t33,54,\t2540,2775,\t11052,31873,\n+41\t10\t0\t0\t0\t0\t0\t0\t+-\tFBtr0300326\t4823\t2799\t2850\tcontig6\t40015\t32155\t32206\t1\t51,\t2799,\t7809,\n+39\t6\t0\t0\t0\t0\t0\t0\t+-\tFBtr0300326\t4823\t2798\t2843\tcontig54\t35008\t16481\t16526\t1\t45,\t2798,\t18482,\n+39\t6\t0\t0\t0\t0\t0\t0\t+-\tFBtr0300326\t4823\t2798\t2843\tcontig53\t50013\t36486\t36531\t1\t45,\t2798,\t13482,\n+51\t15\t0\t0\t0\t0\t0\t0\t+-\tFBtr0300326\t4823\t2787\t2853\tcontig51\t50015\t23765\t23831\t1\t66,\t2787,\t26184,\n+67\t17\t0\t0\t1\t223\t1\t20545\t+-\tFBtr0300326\t4823\t2538\t2845\tcontig44\t50013\t3422\t24051\t2\t36,48,\t2538,2797,\t25962,46543,\n+45\t12\t0\t0\t0\t0\t0\t0\t+-\tFBtr0300326\t4823\t2787\t2844\tcontig32\t40014\t27422\t27479\t1\t57,\t2787,\t12535,\n+47\t10\t0\t0\t0\t0\t0\t0\t+-\tFBtr0300326\t4823\t2801\t2858\tcontig3\t40006\t825\t882\t1\t57,\t2801,\t39124,\n+53\t16\t0\t0\t0\t0\t0\t0\t+-\tFBtr0300326\t4823\t2783\t2852\tcontig3\t40006\t18576\t18645\t1\t69,\t2783,\t21361,\n+76\t14\t0\t0\t1\t224\t1\t159\t+-\tFBtr0300326\t4823\t2538\t2852\tcontig23\t50012\t33494\t33743\t2\t36,54,\t2538,2798,\t16269,16464,\n+40\t8\t0\t0\t0\t0\t0\t0\t+-\tFBtr0300326\t4823\t2805\t2853\tcontig12\t56019\t24590\t24638\t1\t48,\t2805,\t31381,\n+54\t15\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070120\t4901\t1857\t1926\tcontig33\t40016\t5349\t5418\t1\t69,\t1857,\t34598,\n 54\t15\t0\t0\t0\t0\t0\t0\t+-\tFBtr0340081\t4889\t1857\t1926\tcontig33\t40016\t5349\t5418\t1\t69,\t1857,\t34598,\n 54\t15\t0\t0\t0\t0\t0\t0\t+-\tFBtr0340082\t4657\t1613\t1682\tcontig33\t40016\t5349\t5418\t1\t69,\t1613,\t34598,\n-52\t6\t0\t0\t0\t0\t1\t871\t+-\tFBtr0343166\t3140\t318\t376\tcontig62\t50017\t15637\t16566\t2\t18,40,\t318,336,\t33451,34340,\n-76\t29\t0\t0\t1\t534\t0\t0\t+-\tFBtr0343166\t3140\t1891\t2530\tcontig32\t40014\t20318\t20423\t2\t69,36,\t1891,2494,\t19591,19660,\n-107\t32\t0\t0\t2\t498\t2\t41\t+-\tFBtr0343166\t3140\t1902\t2539\tcontig32\t40014\t20291\t20471\t5\t19,39,12,6,63,\t1902,1921,2025,2037,2476,\t19543,19600,19639,19654,19660,\n-72\t12\t0\t0\t2\t544\t2\t69\t+-\tFBtr0343166\t3140\t1902\t2530\tcontig33\t40016\t5316\t5469\t3\t21,27,36,\t1902,2026,2494,\t34547,34605,34664,\n' |
| b |
| diff -r 43803843920b -r 53cf9d25ef39 test-data/dbia3/dbia3_masked.sorted.psl --- a/test-data/dbia3/dbia3_masked.sorted.psl Mon Jul 09 16:31:18 2018 -0400 +++ b/test-data/dbia3/dbia3_masked.sorted.psl Mon Nov 21 11:11:06 2022 +0000 |
| b |
| b'@@ -1,61 +1,61 @@\n-50\t10\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1826\t1886\tcontig67\t44531\t31857\t31917\t1\t60,\t1826,\t12614,\n-38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig25\t75023\t20928\t20973\t1\t45,\t1838,\t54050,\n-38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig50\t40009\t19266\t19311\t1\t45,\t1838,\t20698,\n-38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig51\t50015\t4265\t4310\t1\t45,\t1838,\t45705,\n-39\t9\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig25\t75023\t51622\t51670\t1\t48,\t1838,\t51622,\n-39\t9\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig26\t40013\t1607\t1655\t1\t48,\t1838,\t1607,\n-39\t9\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig32\t40014\t25955\t26003\t1\t48,\t1838,\t14011,\n-39\t9\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig33\t40016\t10953\t11001\t1\t48,\t1838,\t29015,\n-39\t9\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig60\t50013\t16718\t16766\t1\t48,\t1838,\t33247,\n-39\t9\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig61\t40008\t1713\t1761\t1\t48,\t1838,\t38247,\n+40\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig14\t45010\t22563\t22611\t1\t48,\t1838,\t22563,\n+39\t9\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig65\t45013\t12112\t12160\t1\t48,\t1838,\t12112,\n+39\t9\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig64\t40016\t32121\t32169\t1\t48,\t1838,\t32121,\n 39\t9\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig63\t55021\t47126\t47174\t1\t48,\t1838,\t47126,\n-39\t9\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig6\t40015\t23282\t23330\t1\t48,\t1838,\t16685,\n-39\t9\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig64\t40016\t32121\t32169\t1\t48,\t1838,\t32121,\n-39\t9\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig65\t45013\t12112\t12160\t1\t48,\t1838,\t12112,\n-39\t9\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig7\t50017\t13278\t13326\t1\t48,\t1838,\t36691,\n-40\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig13\t45015\t37571\t37619\t1\t48,\t1838,\t37571,\n-40\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig14\t45010\t22563\t22611\t1\t48,\t1838,\t22563,\n-40\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig25\t75023\t51865\t51913\t1\t48,\t1838,\t51865,\n-40\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig26\t40013\t1850\t1898\t1\t48,\t1838,\t1850,\n-40\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig38\t50017\t35343\t35391\t1\t48,\t1838,\t35343,\n+41\t7\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig54\t35008\t7523\t7571\t1\t48,\t1838,\t7523,\n+41\t7\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig54\t35008\t1858\t1906\t1\t48,\t1838,\t1858,\n+40\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig54\t35008\t29934\t29982\t1\t48,\t1838,\t29934,\n+41\t7\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig53\t50013\t27528\t27576\t1\t48,\t1838,\t27528,\n+41\t7\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig53\t50013\t21863\t21911\t1\t48,\t1838,\t21863,\n+40\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig52\t40012\t1146\t1194\t1\t48,\t1838,\t1146,\n+40\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig51\t50015\t31154\t31202\t1\t48,\t1838,\t31154,\n+40\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig50\t40009\t30606\t30654\t1\t48,\t1838,\t30606,\n 40\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig39\t45019\t20340\t20388\t1\t48,\t1838,\t20340,\n 40\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig39\t45019\t7999\t8047\t1\t48,\t1838,\t7999,\n-40\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig50\t40009\t30606\t30654\t1\t48,\t1838,\t30606,\n-40\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig51\t50015\t31154\t31202\t1\t48,\t1838,\t31154,\n-40\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig52\t40012\t1146\t1194\t1\t48,\t1838,\t1146,\n-40\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig54\t35008\t29934\t29982\t1\t48,\t1838,\t29934,\n-40\t8\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig66\t45011\t6949\t6997\t1\t48,\t1838,\t38014,\n-41\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig15\t50014\t19711\t19759\t1\t48,\t1838,\t30255,\n+40\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0070075\t2430\t1838\t1886\tcontig38\t50017\t35343\t35391\t1\t48,\t1838,\t35343,\n+58\t11\t0\t0\t1\t192\t1\t765\t++\tFBtr0070075\t2430\t1838\t2099\tcontig31\t40012\t1075\t1909\t2\t48,21,\t1838,2078,\t1075,1888,\n+58\t11\t0\t0\t1\t192\t1\t765\t++\tFBtr0070075\t2430\t1838\t2099\tcontig30\t70018\t41082\t41916\t2\t48,21,\t1838,2078,\t41082,41895,\n+40\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr00'..b'g44\t50013\t3422\t24051\t2\t36,48,\t2538,2797,\t25962,46543,\n-68\t16\t0\t0\t1\t231\t1\t17935\t++\tFBtr0300326\t4823\t2538\t2853\tcontig40\t60015\t6537\t24556\t2\t36,48,\t2538,2805,\t6537,24508,\n-68\t16\t0\t0\t1\t231\t1\t292\t++\tFBtr0300326\t4823\t2538\t2853\tcontig58\t50011\t15076\t15452\t2\t27,57,\t2538,2796,\t15076,15395,\n-76\t14\t0\t0\t1\t224\t1\t159\t+-\tFBtr0300326\t4823\t2538\t2852\tcontig23\t50012\t33494\t33743\t2\t36,54,\t2538,2798,\t16269,16464,\n-63\t18\t0\t0\t1\t215\t1\t773\t++\tFBtr0300326\t4823\t2539\t2835\tcontig55\t40015\t6868\t7722\t2\t33,48,\t2539,2787,\t6868,7674,\n+39\t9\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig61\t40008\t1713\t1761\t1\t48,\t1838,\t38247,\n+39\t9\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig60\t50013\t16718\t16766\t1\t48,\t1838,\t33247,\n+39\t9\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig6\t40015\t23282\t23330\t1\t48,\t1838,\t16685,\n+38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig51\t50015\t4265\t4310\t1\t45,\t1838,\t45705,\n+38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig50\t40009\t19266\t19311\t1\t45,\t1838,\t20698,\n+39\t9\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig33\t40016\t10953\t11001\t1\t48,\t1838,\t29015,\n+39\t9\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig32\t40014\t25955\t26003\t1\t48,\t1838,\t14011,\n+38\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1883\tcontig25\t75023\t20928\t20973\t1\t45,\t1838,\t54050,\n+41\t7\t0\t0\t0\t0\t0\t0\t+-\tFBtr0070075\t2430\t1838\t1886\tcontig15\t50014\t19711\t19759\t1\t48,\t1838,\t30255,\n+69\t18\t0\t0\t1\t202\t1\t20788\t+-\tFBtr0300326\t4823\t2540\t2829\tcontig64\t40016\t8089\t28964\t2\t33,54,\t2540,2775,\t11052,31873,\n 69\t18\t0\t0\t1\t202\t1\t20788\t+-\tFBtr0300326\t4823\t2540\t2829\tcontig63\t55021\t23094\t43969\t2\t33,54,\t2540,2775,\t11052,31873,\n-69\t18\t0\t0\t1\t202\t1\t20788\t+-\tFBtr0300326\t4823\t2540\t2829\tcontig64\t40016\t8089\t28964\t2\t33,54,\t2540,2775,\t11052,31873,\n-62\t13\t0\t0\t1\t224\t1\t5747\t++\tFBtr0300326\t4823\t2545\t2844\tcontig56\t55020\t11121\t16943\t2\t30,45,\t2545,2799,\t11121,16898,\n-57\t21\t0\t0\t0\t0\t0\t0\t++\tFBtr0300326\t4823\t2776\t2854\tcontig41\t60014\t49022\t49100\t1\t78,\t2776,\t49022,\n-45\t12\t0\t0\t0\t0\t0\t0\t+-\tFBtr0300326\t4823\t2787\t2844\tcontig32\t40014\t27422\t27479\t1\t57,\t2787,\t12535,\n-51\t15\t0\t0\t0\t0\t0\t0\t+-\tFBtr0300326\t4823\t2787\t2853\tcontig51\t50015\t23765\t23831\t1\t66,\t2787,\t26184,\n-46\t11\t0\t0\t0\t0\t0\t0\t++\tFBtr0300326\t4823\t2796\t2853\tcontig57\t60013\t40402\t40459\t1\t57,\t2796,\t40402,\n-38\t7\t0\t0\t0\t0\t0\t0\t++\tFBtr0300326\t4823\t2798\t2843\tcontig60\t50013\t39781\t39826\t1\t45,\t2798,\t39781,\n-39\t6\t0\t0\t0\t0\t0\t0\t++\tFBtr0300326\t4823\t2798\t2843\tcontig14\t45010\t5355\t5400\t1\t45,\t2798,\t5355,\n-39\t6\t0\t0\t0\t0\t0\t0\t+-\tFBtr0300326\t4823\t2798\t2843\tcontig53\t50013\t36486\t36531\t1\t45,\t2798,\t13482,\n+41\t10\t0\t0\t0\t0\t0\t0\t+-\tFBtr0300326\t4823\t2799\t2850\tcontig6\t40015\t32155\t32206\t1\t51,\t2799,\t7809,\n 39\t6\t0\t0\t0\t0\t0\t0\t+-\tFBtr0300326\t4823\t2798\t2843\tcontig54\t35008\t16481\t16526\t1\t45,\t2798,\t18482,\n-41\t10\t0\t0\t0\t0\t0\t0\t+-\tFBtr0300326\t4823\t2799\t2850\tcontig6\t40015\t32155\t32206\t1\t51,\t2799,\t7809,\n-45\t9\t0\t0\t0\t0\t0\t0\t++\tFBtr0300326\t4823\t2799\t2853\tcontig13\t45015\t20364\t20418\t1\t54,\t2799,\t20364,\n-46\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0300326\t4823\t2799\t2853\tcontig37\t50013\t25795\t25849\t1\t54,\t2799,\t25795,\n-46\t8\t0\t0\t0\t0\t0\t0\t++\tFBtr0300326\t4823\t2799\t2853\tcontig38\t50017\t10792\t10846\t1\t54,\t2799,\t10792,\n+39\t6\t0\t0\t0\t0\t0\t0\t+-\tFBtr0300326\t4823\t2798\t2843\tcontig53\t50013\t36486\t36531\t1\t45,\t2798,\t13482,\n+51\t15\t0\t0\t0\t0\t0\t0\t+-\tFBtr0300326\t4823\t2787\t2853\tcontig51\t50015\t23765\t23831\t1\t66,\t2787,\t26184,\n+67\t17\t0\t0\t1\t223\t1\t20545\t+-\tFBtr0300326\t4823\t2538\t2845\tcontig44\t50013\t3422\t24051\t2\t36,48,\t2538,2797,\t25962,46543,\n+45\t12\t0\t0\t0\t0\t0\t0\t+-\tFBtr0300326\t4823\t2787\t2844\tcontig32\t40014\t27422\t27479\t1\t57,\t2787,\t12535,\n 47\t10\t0\t0\t0\t0\t0\t0\t+-\tFBtr0300326\t4823\t2801\t2858\tcontig3\t40006\t825\t882\t1\t57,\t2801,\t39124,\n-39\t9\t0\t0\t0\t0\t0\t0\t++\tFBtr0300326\t4823\t2805\t2853\tcontig56\t55020\t44922\t44970\t1\t48,\t2805,\t44922,\n-39\t9\t0\t0\t0\t0\t0\t0\t++\tFBtr0300326\t4823\t2805\t2853\tcontig57\t60013\t14909\t14957\t1\t48,\t2805,\t14909,\n+76\t14\t0\t0\t1\t224\t1\t159\t+-\tFBtr0300326\t4823\t2538\t2852\tcontig23\t50012\t33494\t33743\t2\t36,54,\t2538,2798,\t16269,16464,\n 40\t8\t0\t0\t0\t0\t0\t0\t+-\tFBtr0300326\t4823\t2805\t2853\tcontig12\t56019\t24590\t24638\t1\t48,\t2805,\t31381,\n-42\t12\t0\t0\t0\t0\t0\t0\t++\tFBtr0300326\t4823\t2805\t2859\tcontig46\t50012\t18047\t18101\t1\t54,\t2805,\t18047,\n' |
| b |
| diff -r 43803843920b -r 53cf9d25ef39 tool_dependencies.xml --- a/tool_dependencies.xml Mon Jul 09 16:31:18 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,27 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <!-- required tools: - - blat - - sort - - pslReps - - faPolyASizes - - pslCDnaFilter - --> - <package name="ucsc_tools_340_for_BLAT" version="1.0"> - <install version="1.0"> - <actions_group> - <actions architecture="x86_64" os="linux"> - <action type="download_by_url">http://old-gep.wustl.edu/~galaxy/package_ucsc_tools_340_for_BLAT.tar.gz</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR/bin</destination_directory> - </action> - </actions> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions_group> - </install> - <readme>The tools and utilities were created by the UCSC Genome Bioinformatics Group</readme> - </package> -</tool_dependency> \ No newline at end of file |