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Commit message:
planemo upload for repository https://github.com/goeckslab/trfBig commit 97fd3895fbafc69df1a1c4092f261ba23fc0bd0b-dirty |
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added:
test-data/dbia3.bed test-data/dbia3.fasta tool_dependencies.xml trfBig.xml |
| b |
| diff -r 000000000000 -r ba819b65bef3 test-data/dbia3.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dbia3.bed Mon May 01 17:34:42 2017 -0400 |
| b |
| b'@@ -0,0 +1,66063 @@\n+contig1\t9130\t9428\ttrf\t163\t1.8\t164\t86\t2\t438\t36\t12\t13\t37\t1.82\tAAAAAAAATTATATCTTCGGTGTTTTTCAACATACAACCTCCTAAGCTTGGAAATAACATTTCTTAATCAGTTCTGAATTTCGAATTAAATTTTTATCAAAATCGGACAACTATACCATATAGCTGTCATAGGAAGGATTGGATAATTAGTGGTAAAATAATAT\n+contig1\t15707\t15757\ttrf\t20\t2.5\t19\t83\t9\t55\t32\t12\t2\t54\t1.49\tTATATCATTTATATCTCAG\n+contig1\t16261\t16302\ttrf\t12\t3.4\t12\t89\t0\t64\t2\t36\t24\t36\t1.69\tTCCGTCTGTCCG\n+contig1\t23387\t23483\ttrf\t45\t2.2\t45\t92\t1\t158\t19\t22\t30\t27\t1.98\tTCGGCGAAGAAATGTGCCACTTCGGCGGCACTTCTTGGAGTCACT\n+contig1\t23451\t23520\ttrf\t24\t2.9\t24\t80\t0\t75\t15\t26\t27\t30\t1.96\tTTCGGCGACACTTCTTGAAGTCAG\n+contig1\t24200\t24233\ttrf\t15\t2.2\t15\t94\t0\t57\t51\t12\t15\t21\t1.75\tAAACAATGGAATGCT\n+contig1\t29159\t29628\ttrf\t162\t2.9\t160\t80\t8\t518\t37\t12\t11\t38\t1.80\tGGAAAACATGAAATAAAAATTATATCTTTCGTGTTTTTTAACATATACCTTCTAAGCTTGAAAATAACATTTTTTATTTGTTCTGAATTTCGAATTAAATTTTATCAAAATCGGACGACTATATCATATAGCTGTCATAGGAACAATCGGAAAATAAGTA\n+contig1\t37571\t37606\ttrf\t8\t4.4\t8\t88\t0\t52\t31\t25\t42\t0\t1.55\tGACGGACA\n+contig1\t38436\t38491\ttrf\t8\t6.9\t8\t79\t8\t58\t0\t38\t27\t34\t1.57\tTGTCCGTC\n+contig1\t38436\t38491\ttrf\t12\t4.6\t12\t81\t0\t65\t0\t38\t27\t34\t1.57\tTGTCCGTCCGTC\n+contig1\t38436\t38491\ttrf\t20\t3.1\t18\t80\t17\t69\t0\t38\t27\t34\t1.57\tTGTCCGTCTGTCCGTCCG\n+contig1\t43116\t43168\ttrf\t2\t26.0\t2\t96\t0\t95\t48\t0\t1\t50\t1.12\tTA\n+contig2\t540\t590\ttrf\t20\t2.5\t19\t83\t9\t55\t32\t12\t2\t54\t1.49\tTATATCATTTATATCTCAG\n+contig2\t1094\t1135\ttrf\t12\t3.4\t12\t89\t0\t64\t2\t36\t24\t36\t1.69\tTCCGTCTGTCCG\n+contig2\t8220\t8316\ttrf\t45\t2.2\t45\t92\t1\t158\t19\t22\t30\t27\t1.98\tTCGGCGAAGAAATGTGCCACTTCGGCGGCACTTCTTGGAGTCACT\n+contig2\t8284\t8353\ttrf\t24\t2.9\t24\t80\t0\t75\t15\t26\t27\t30\t1.96\tTTCGGCGACACTTCTTGAAGTCAG\n+contig2\t9033\t9066\ttrf\t15\t2.2\t15\t94\t0\t57\t51\t12\t15\t21\t1.75\tAAACAATGGAATGCT\n+contig2\t13992\t14461\ttrf\t162\t2.9\t160\t80\t8\t518\t37\t12\t11\t38\t1.80\tGGAAAACATGAAATAAAAATTATATCTTTCGTGTTTTTTAACATATACCTTCTAAGCTTGAAAATAACATTTTTTATTTGTTCTGAATTTCGAATTAAATTTTATCAAAATCGGACGACTATATCATATAGCTGTCATAGGAACAATCGGAAAATAAGTA\n+contig2\t22404\t22439\ttrf\t8\t4.4\t8\t88\t0\t52\t31\t25\t42\t0\t1.55\tGACGGACA\n+contig2\t23269\t23324\ttrf\t8\t6.9\t8\t79\t8\t58\t0\t38\t27\t34\t1.57\tTGTCCGTC\n+contig2\t23269\t23324\ttrf\t12\t4.6\t12\t81\t0\t65\t0\t38\t27\t34\t1.57\tTGTCCGTCCGTC\n+contig2\t23269\t23324\ttrf\t20\t3.1\t18\t80\t17\t69\t0\t38\t27\t34\t1.57\tTGTCCGTCTGTCCGTCCG\n+contig2\t27949\t28001\ttrf\t2\t26.0\t2\t96\t0\t95\t48\t0\t1\t50\t1.12\tTA\n+contig2\t38280\t38311\ttrf\t16\t1.9\t16\t93\t0\t53\t41\t19\t6\t32\t1.77\tTACATACATACATATG\n+contig3\t3265\t3296\ttrf\t16\t1.9\t16\t93\t0\t53\t41\t19\t6\t32\t1.77\tTACATACATACATATG\n+contig3\t17933\t17958\ttrf\t10\t2.5\t10\t100\t0\t50\t60\t8\t0\t32\t1.26\tATATAAACAT\n+contig3\t19067\t19124\ttrf\t28\t2.0\t28\t100\t0\t114\t43\t14\t10\t31\t1.79\tAATTAAATTTTATCAAAATCGGACGACT\n+contig3\t23368\t23418\ttrf\t2\t25.0\t2\t100\t0\t100\t50\t0\t0\t50\t1.00\tAT\n+contig3\t24889\t25322\ttrf\t160\t2.7\t161\t80\t6\t452\t36\t12\t12\t38\t1.82\tAATATTAAAAATTATATCTTTGGTGTTTTTTAACATATAACCTTCTAAGCTTGGAAATAACATTTTTTATTTGGTTTAATTTCGAATTAAATTTTATTAAAATCGGACGACCATATCATACAGCTCCCATAGAAACAATCGGAAAATTAGTCGGAAACATG\n+contig3\t26816\t26900\ttrf\t18\t5.0\t16\t83\t13\t89\t20\t5\t0\t73\t1.03\tTTTTTTTATATATTTT\n+contig3\t26816\t26887\ttrf\t18\t4.1\t17\t84\t12\t90\t19\t4\t0\t76\t0.96\tTTTTTTTATATATTTTT\n+contig3\t26816\t26900\ttrf\t15\t5.2\t15\t79\t16\t71\t20\t5\t0\t73\t1.03\tTTTTTTTATATATAT\n+contig3\t26820\t26887\ttrf\t17\t3.7\t19\t80\t20\t74\t20\t4\t0\t74\t0.99\tTTTATATATTTTTTTTTCA\n+contig3\t29468\t29515\ttrf\t25\t2.0\t23\t84\t12\t60\t34\t0\t17\t48\t1.47\tATTATAATTATGATGTTATGATG\n+contig3\t38756\t38791\ttrf\t10\t3.6\t10\t92\t7\t63\t40\t0\t0\t60\t0.97\tATTTATTTAA\n+contig3\t38758\t38788\ttrf\t9\t3.2\t9\t95\t4\t51\t40\t0\t0\t60\t0.97\tTTATTTAAA\n+contig4\t7931\t7956\ttrf\t10\t2.5\t10\t100\t0\t50\t60\t8\t0\t32\t1.26\tATATAAACAT\n+contig4\t9065\t9122\ttrf\t28\t2.0\t28\t100\t0\t114\t43\t14\t10\t31\t1.79\tAATTAAATTTTATCAAAATCGGACGACT\n+contig4\t13366\t13416\ttrf\t2\t25.0\t2\t100\t0\t100\t50\t0\t0\t50\t1.00\tAT\n+contig4\t14887\t15320\ttrf\t160\t2.7\t161\t80\t6\t452\t36\t12\t12\t38\t1.82\tAATATTAAAAATTATATCTTTGGTGTTTTTTAACATATAACCTTCTAAGCTTGGAAATAACATTTTTTATTTGGTTTAATTTCGAATTAAATTTTATTAAAATCGGACGACCATATCATACAGCTCCCATAGAAACAATCGGAAAATTAGTCGGAAACATG\n+contig4\t16814\t16898\ttrf\t18\t5.0\t16\t83\t13\t89\t20\t5\t0\t73\t1.03\tTTTTTTTATATATTTT\n+contig4\t16814\t16885\ttrf\t18\t4.1\t17\t84\t12\t90\t19\t4\t0\t76\t0.96\tTTTTTTTATATATTTTT\n+contig4\t16814\t16898\ttrf\t15\t5.2\t15\t79\t16\t71\t20\t5\t0\t73\t1.03\tTTTTTTTATATAT'..b'ccactggacccgttggatagcgtc\n+ggcacttttctgtttggtgccattcactggtcactagtaggaccgctctg\n+cctattaaaataggagtgctgcttagaatttatttcagcaagacagccgt\n+aagatatatatgaatagtatttaacggcagtggcagaggcctttacaata\n+taaggctttacgggattttaaacaatgaaaaacaaaaatatttttataga\n+gtcgagataaaatactttttacaataaatactaagtatttttaaaagata\n+aaaatatttaaaagtaaatactgaatattttaacaggtgttaagtactgg\n+gaactgtgactaaggacggcggtatatcgctaccataatatttttaaagg\n+aactgaatactgaaagatgtgaccaaaatggtagaatatcgctaacgaaa\n+atcacagacgcaaatatcgatagtggcctagagacccgatatcgccgccg\n+tgattatcgatgaaactacagctgagctgcttgtttacattctaaagtta\n+aaatttttaaaaatttccaatacaaaaaaaaattcttcgtattaacacgg\n+ctgtttgccggtaagatctgaagtggattcaagttgcagcaccctcagga\n+aaagaataaattattataatataataatataatataaagaatttaaattc\n+gaaccaaacgcggtatgtcactcttcatttagagaatttgtggctttgtt\n+ttgtacaaaaaactattcttttttcttgaaaattagcatcaagaatttat\n+tgccaaaacagaacgcaattctgctaaatctggttaccctgccaaatggc\n+tggccgttctgtgcattcaataacacaagctaacggcttacggcacattc\n+ggaaagatccaaaagaatttctattccggcattttttatgtattatcgtc\n+caatttttgtatgtgtattcattcttttggctgtccgttattaagctttt\n+cttatccacataagctgaccagctgccaaaaagccgaccgttttgtgcag\n+ccaataacccaagctaactatcaacagcaatttcgaaaaatccagaagaa\n+gctatccttcggcaattttttcttatattataatttttttgtcacaattt\n+tttgtcaaaaaatcgacaataattaagtgtttacattttaatgcgattta\n+attggaaatttgaattcgaatcaaacgcggtgtcactctacatatggaca\n+atttgtggctacaaaattagttgaaagtgcatgtttttttttaagtgaaa\n+taaaacaaaaacagcaataacaggccaaaatgttgttttataaataaata\n+cttacatatccgcatataaatatgaatgaaaaaaaaaacagcaagactgg\n+gccaaaatattgttctttaatatgtaaataaatacatatctacatataca\n+tatgtggacaaaagtgttaaaattagttaatagtgcatgttttttaaatg\n+aaaaaataaaacaaaaaaagcaagcaaatataaattatattccacacaca\n+tttacaataatttcaaactacgctaaaaatacccaacagaaaaaacatag\n+aaaggtaaacaaaatacaagaatatcaaaaaaaatctaattttcacgttg\n+ttgtggccggtaccaccggtcatacatacatatagatacatatttagatt\n+ctcacaaaaagaatagaaaattaccgctaatttccttatatacgtttttg\n+ttttcagtgttttgaaatagtatttttcaaacaaaaaacaatacaaaagg\n+gttaaaaaaattgttcgattggctttaacatactaattaaaaaaaatcac\n+aattttttggcaaaatatcgaaaaaaattaagtgtttacatttttatgcg\n+aattatttggaaatttaaataagaacccaacgcggtttgtcactctacat\n+atggacaatttgtggctttgttttgaacaaaaaatgaatttttttttact\n+caaaattaacaagaagaaacagtaatgcgggttttgatcgcaattctgct\n+aaatcgaatttccgtgcccaaaggctgacctttttgtgcagcaaatagcc\n+caagctaataatctacagcaatttcttaaagaccgaaaatgtatcaactt\n+cggcaaaatatgaaaatttaacatttatttttcaacattttttgccaaat\n+aatcgacaaaaatttcagtgtcccgatttggatgcgaattaattgaggac\n+aattgtgactttgttttgtaaaaaaactattttttttactgaaaattaca\n+atcaagaatctaaggccaaatcagaatattttcactgcggttttttgatc\n+gcaattctgctaaatcgggttccgtgccaaaaagctgactatttttttta\n+ctgagaattagcatcaagaatttattgccaaaacagaacgcaattctgct\n+aaatcgggttgccctgccaaaaggctggccgttttgcgcattcaataaca\n+caagctaacggtttacagcacattcggaaagatccaaaagaatttctatt\n+tcggcattttttatgtattatcgtctaattttggtatgtgtattcattct\n+tttggctgtccgttattaagctgcttttcttattcacatattcaatggcg\n+cagtacataaaaagaatgaaccgtggttttcttgccctctccatctccct\n+ctaccacttcccctctcaacaactatctcacgcactctgtcccttctcgt\n+nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn\n+nnnnnnnnnnnnnnnnnnnnnnnnnnnnattctctctgtcgcgctcgctc\n+tctcaacatgcctttcgcaccgtatctcttcgtttctctgtatgcttgct\n+ctcttaatttaagtttctctttctttgtgttcaatatctttcgcgctcgt\n+gactcctattgaccggactctgagcggtgctcattaagagtggagttttc\n+gatgatggcgggtggcgcgaacgagaattttttacataaaggtaagttgc\n+caattcttttttaaatgtgacatacagcatgcatattttatttattgtaa\n+ttatatgtgaaagaataaaattatatgtacttttatctaatctattgcat\n+ctattttttcacaggtaaacgagtcacacgagaagtaaaacacaaacaca\n+aggatcaaaataaaattcaggtgagtgaacgaacgtgttgaaagtagtta\n+atagtgcatgtctatttaagtgtaagaaacaaaaaagacacaaatgggcc\n+aataattcgtttctttaatagataactgcctatattatgttcaaactatg\n+ctaaaaagacccaaaaggaaaacataaagtatataccttgcaaaatgaat\n+aaaaagaaatcatatatattcatatacgtttgaccggtaccaccggtcat\n+acatacataaacataaacacaaaaagactagaatataaataccatatttt\n+tgattggcttaaaaatggcacaaaaaaaagataaaaactagagtgtctag\n+ctttaagtgacaatcgactcggaaaatgatcaagaaataaatgaaaaatt\n+tgtcttgcggctttttggtcgcaattctaaatcggtttgtatgtatgtca\n+ctcttcatgtatacaatttggtggctttgtattccacaaaagtcacagta\n+gtcacaaaagttttttttactgaaaattaccatcaagagtctatggccaa\n+atcagaatattttcactgcggttttttatttcaattctgctaaatcgggt\n+ttccgtgccaaaaagcttttgcagccaacaacaatattcaattttttggc\n+aaaaaatcgacaaaaaaatt\n' |
| b |
| diff -r 000000000000 -r ba819b65bef3 test-data/dbia3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dbia3.fasta Mon May 01 17:34:42 2017 -0400 |
| b |
| b'@@ -0,0 +1,66784 @@\n+>contig1\n+AAAACTAATTTTATCAAAATCGGACAACTATATCATATAGCTGCCATACG\n+AACGATCGGAAAATTGGTAAGTAAATAATTAAAAATATTATATCTTTGGT\n+GTGTTTTTGGAAATAACATTTTTTAATATGTTTTGAATTTTGAATTAAAT\n+TCTATCAAAATCGGACGACTATATCATATAGCTGCCATACAAACGATCGG\n+AAAATTGGTGAATAAATAATATGAAAAAATTATATCTTTGGTTATTTTTT\n+AGACAAATAACCTCCAACGCTTGGAAATAACATTTTTTAATTAGTTATAA\n+ATTTGATATTTTAATTTTATCAAAATCGGACGAATATAGCATATAGCTGT\n+TAAAATAATATGAAACAAATTATAGCTCCGGTGTTTTTTACATATTATCT\n+TATACTATTGGGAAAATAGTTTATTATATTTTAAAGAATTTCCAATTAAA\n+CTCTAACATATAGCTTTCAAAGAAACGGTCAAAAAAGTAAAGAAATCATT\n+TTTTTTTAACATCACTGAAGCTAGAAACAATCCTTAAAAATGTAACATGG\n+TGTTAGTAGCATTGAAAATTGCTTATAACTGCAAAGGGAAAACAAACATC\n+GGCTTGCCGAATGTAATTTCCATTCTTGTTTGACTTGAGTTTATAACTTA\n+CAATTATGGTAAGGTGCCTGATTTTGGTTTTTGCCATACGGTATGTGGTA\n+GTTATCATTTTGCCGTGCTATAAGTGACATCACAGCCGATTCTTTTACTC\n+CATAATGGGCCAATGTGTTGAGGCGTTTCCATCCATTTATTGTTTTTGTA\n+GTTAGGTCTTCATCTTGTAATGTGAGATGACCTCCTCTTCCATGCCTCCA\n+TTCTAAGTCAACTTCGTGCACAGATGGTCTCATAGAAAACGGAGTATTTT\n+TAAAAATTGCGTCCAAAATTTTTAATTTAACTTGCGATATGGTATCCAAA\n+TCGTTTACACGACATTGGACTTTTTCATCAAGATCATCTTGTAAAATGTG\n+CAAAATTACAACAGAATGGGTAACTTGTTCGTGGAGAAGTCGTTCCTCTG\n+AAAGTGAATAACGAGCATCGTGGGTTATTGCGTCCACCAAACCCTTTTCA\n+ATTTGATGCTTAATTGCCTTGAACAGCAAAAATAAATTAGATCCAGCATA\n+TTCTTTTAGGTAGTCGTACATACAAATTGCTAAGTAGTTTGTTAACATTT\n+TTTCAACTACGCTCTCAGTGCGTCGTAGCATTAGCTGAGGATGCTTGCTG\n+GCGAGCGATTTGTCAATTAATCGCAATAAAAGGGACTTTAAAATTTCCGT\n+CGCATATTCCATTTTGTTCATTAGAACAACCATAAGTAAAGAGGCGACGT\n+TAACTCGATCGCGAATTGAGAAAGATGACCGTTGAGCTTCTAAAGTTTCT\n+ATGAACAATAGTAAAAAATATTTGTTTCCAATAAGTTGCTCGAATTGTAT\n+CATAGCTGCATCATAGTTAGTGTGCGGGCTACTTCCACAAAATTTTCGGG\n+AGTTTAGAATAGGATGATCTGATACACCGGGAAAGAAAACTTTCATAATG\n+TAATTGACGTGATCTAACGTTGGTATACCGGTGCTCTCCAAATCTGCTGT\n+TAGATCGGTCATGTCCGTTTGGAGCTCAGCAAATGCCTGTTTACACTCAG\n+AACGAACGTTGCTTTCCAATGTTATCATCTGTATCTGAATTCGTTTGTAT\n+TCCCGTTCTGCTTGGGTCGATTTCCTTCTAAATATTATTAGTACGACAAC\n+CAAAACGATGACAAGCACTGCAACTGTCAATATAACGACAAACATGGCAT\n+GTGAAAAAACATAGGGTTTATTTAAATCATATTTCAAATATCCTATGGCG\n+AAACGAAGATTTCGCCCTACTTTAACCACAACTAGAGGTAAATCTGTCGA\n+TTGATCCACACCATTTTCATCAGTTGGGAGTGGTTGATGTTCCGGTGGAA\n+TGCACAAAAGTTGAGTTAGTGTAAGGCTTGTTATATTGCATTGAGTAGTA\n+CCAATGGTTACATTAACGTCGTATTCATCAGCTGCCAAATTTAGTAGCTC\n+GCCTTCAATAACCAAGCTGTCACCCTTGTATAGTTTAATTCCGTCATTTG\n+GAAATGGTAAATATTTTGGATCGGCTAAATAAACAATAGTGCTCCTGATA\n+TCATGAAAGTATTTATTTAGATCTCGAACAAGCTGTACATTGTCCATTAC\n+AAAACTAAGTTGTAAATTCAGTTGCGTTTCATGGACCTTTACAAAAGTTG\n+TAACATCCATATTATTATTGACGAAATAGCTAGGCGCAGTTCCCCCTGTT\n+GTGTATATATGAAAGTTGTCTACGAAGTCTGCTTTTCGCTTTCGTCTAGA\n+ATATTCGTTCTGATGCGCACTTTCATTTTTAAAGTCAAATTCCGAATCCA\n+TCACTCTGTTAGAACTTTTAAATGCTTGAAATTTATCATTTACCGGAGGA\n+GATGGGCATTCCATTTGATTTGAATTGATTACTACGCAAGATGTTTTGTT\n+TACTCTTTCATTATCAAAAAAAACTTCAAGTTCAGGCTTTTGAATTGAAT\n+TAAGATACATTCCATGAACGGTCAGAACGCGACCACCACTTACAAAACTG\n+CGTAAAGGCTTAATCTGCATTATACGCGGGTCTTGGGTATAGTTAAAAAT\n+AGAACAGGGCTGCCTTGGTAACGTACGAAATTGGTATGAACCGAAATTAC\n+TTCGAGTTAGATTTTTATTGGGTATAGTTGCGGGTGAGATATGACATTCT\n+AAAGTTCGGTTGGCACCGTCAATAAGAAGGTGTAGAGACCGTATTGGTTC\n+TGGCTGGGTCGCCTCTGATGTAGTACTACTAACTTGAGTTGAAGAAGCTT\n+GTGTAACGTTTATATGACACTCGTACTCATCTAAATATGCTCGCATGGTT\n+GATCCAATGTTCAAAAACTTTCCTATTAACGACAATTGTGTTCCTCCCGA\n+CCTGGGCCCAATCGTGGGATATAATCCTGTTAGCAAAACATTCTTAAAGT\n+GAAATTGTACACTAGATTCAGTATACCCTGCATCATTTGCAACCTTTATA\n+GGCGCTGACATTTCATACATCACTGCTCCAGTGCGGCATTCGATCTTTAC\n+AGAAATTTGGTAGTTGACTAGTTCACAAGGCACAGACCCAATAAATATTT\n+TTCCACGCACATCTCCTTCGCGAATGCCCAAATTACTGCCTTCAATTGTA\n+ATAAGGGTACCACCCTCAATAGGTCCAGATAACGGTTTAATAATATCGAT\n+CCTTGGTAAAGGGCACTCGTTTTCTTTAGTTGTTTTTGATCCTGCACTAA\n+TAGCACGATCACTGTCTGCTATGCAAGTCTCGTTATATACACATGAGTTG\n+CTGCACCAAGCACATTGGTATTTTGGATCACGAGTGACACACAAACTGCA\n+ATCAGCATGATCCCGATGTGAGCCCAGTACGTCGCATTTATATAATGTAA\n+CAATCGCCGTGTCCACATAGTGCTGGAAATTCCATGTAATTACAACCTTT\n+GCTTGGTATTCATGTGTATTAGTCTCGTAGAAATAAGGTGTTTTTTCACA\n+AACAACAATCTTGTTTGACTCAATGTGGGCAGGCAATAGCATCTGAGCAG\n+CTTCAATATGAACTGTACACAAGAATCCAGCGTGAGCGCTTTTGGGTTTT\n+GGTAAGTTTTCTATCTCTAAACGAATTTCTTTTGGCACCCGCACCGGTAA\n+AAGAATCGCCGGACGATTGCTTTTTAAATGGGGGCATTGACCAACACTAG\n+TTACCGAATTTTCTATATTACGACATTGTATTGATTGATGGACACATTTA\n+TTGTCAAAAATACACC'..b'CCACTGGACCCGTTGGATAGCGTC\n+GGCACTTTTCTGTTTGGTGCCATTCACTGGTCACTAGTAGGACCGCTCTG\n+CCTATTAAAATAGGAGTGCTGCTTAGAATTTATTTCAGCAAGACAGCCGT\n+AAGATATATATGAATAGTATTTAACGGCAGTGGCAGAGGCCTTTACAATA\n+TAAGGCTTTACGGGATTTTAAACAATGAAAAACAAAAATATTTTTATAGA\n+GTCGAGATAAAATACTTTTTACAATAAATACTAAGTATTTTTAAAAGATA\n+AAAATATTTAAAAGTAAATACTGAATATTTTAACAGGTGTTAAGTACTGG\n+GAACTGTGACTAAGGACGGCGGTATATCGCTACCATAATATTTTTAAAGG\n+AACTGAATACTGAAAGATGTGACCAAAATGGTAGAATATCGCTAACGAAA\n+ATCACAGACGCAAATATCGATAGTGGCCTAGAGACCCGATATCGCCGCCG\n+TGATTATCGATGAAACTACAGCTGAGCTGCTTGTTTACATTCTAAAGTTA\n+AAATTTTTAAAAATTTCCAATACAAAAAAAAATTCTTCGTATTAACACGG\n+CTGTTTGCCGGTAAGATCTGAAGTGGATTCAAGTTGCAGCACCCTCAGGA\n+AAAGAATAAATTATTATAATATAATAATATAATATAAAGAATTTAAATTC\n+GAACCAAACGCGGTATGTCACTCTTCATTTAGAGAATTTGTGGCTTTGTT\n+TTGTACAAAAAACTATTCTTTTTTCTTGAAAATTAGCATCAAGAATTTAT\n+TGCCAAAACAGAACGCAATTCTGCTAAATCTGGTTACCCTGCCAAATGGC\n+TGGCCGTTCTGTGCATTCAATAACACAAGCTAACGGCTTACGGCACATTC\n+GGAAAGATCCAAAAGAATTTCTATTCCGGCATTTTTTATGTATTATCGTC\n+CAATTTTTGTATGTGTATTCATTCTTTTGGCTGTCCGTTATTAAGCTTTT\n+CTTATCCACATAAGCTGACCAGCTGCCAAAAAGCCGACCGTTTTGTGCAG\n+CCAATAACCCAAGCTAACTATCAACAGCAATTTCGAAAAATCCAGAAGAA\n+GCTATCCTTCGGCAATTTTTTCTTATATTATAATTTTTTTGTCACAATTT\n+TTTGTCAAAAAATCGACAATAATTAAGTGTTTACATTTTAATGCGATTTA\n+ATTGGAAATTTGAATTCGAATCAAACGCGGTGTCACTCTACATATGGACA\n+ATTTGTGGCTACAAAATTAGTTGAAAGTGCATGTTTTTTTTTAAGTGAAA\n+TAAAACAAAAACAGCAATAACAGGCCAAAATGTTGTTTTATAAATAAATA\n+CTTACATATCCGCATATAAATATGAATGAAAAAAAAAACAGCAAGACTGG\n+GCCAAAATATTGTTCTTTAATATGTAAATAAATACATATCTACATATACA\n+TATGTGGACAAAAGTGTTAAAATTAGTTAATAGTGCATGTTTTTTAAATG\n+AAAAAATAAAACAAAAAAAGCAAGCAAATATAAATTATATTCCACACACA\n+TTTACAATAATTTCAAACTACGCTAAAAATACCCAACAGAAAAAACATAG\n+AAAGGTAAACAAAATACAAGAATATCAAAAAAAATCTAATTTTCACGTTG\n+TTGTGGCCGGTACCACCGGTCATACATACATATAGATACATATTTAGATT\n+CTCACAAAAAGAATAGAAAATTACCGCTAATTTCCTTATATACGTTTTTG\n+TTTTCAGTGTTTTGAAATAGTATTTTTCAAACAAAAAACAATACAAAAGG\n+GTTAAAAAAATTGTTCGATTGGCTTTAACATACTAATTAAAAAAAATCAC\n+AATTTTTTGGCAAAATATCGAAAAAAATTAAGTGTTTACATTTTTATGCG\n+AATTATTTGGAAATTTAAATAAGAACCCAACGCGGTTTGTCACTCTACAT\n+ATGGACAATTTGTGGCTTTGTTTTGAACAAAAAATGAATTTTTTTTTACT\n+CAAAATTAACAAGAAGAAACAGTAATGCGGGTTTTGATCGCAATTCTGCT\n+AAATCGAATTTCCGTGCCCAAAGGCTGACCTTTTTGTGCAGCAAATAGCC\n+CAAGCTAATAATCTACAGCAATTTCTTAAAGACCGAAAATGTATCAACTT\n+CGGCAAAATATGAAAATTTAACATTTATTTTTCAACATTTTTTGCCAAAT\n+AATCGACAAAAATTTCAGTGTCCCGATTTGGATGCGAATTAATTGAGGAC\n+AATTGTGACTTTGTTTTGTAAAAAAACTATTTTTTTTACTGAAAATTACA\n+ATCAAGAATCTAAGGCCAAATCAGAATATTTTCACTGCGGTTTTTTGATC\n+GCAATTCTGCTAAATCGGGTTCCGTGCCAAAAAGCTGACTATTTTTTTTA\n+CTGAGAATTAGCATCAAGAATTTATTGCCAAAACAGAACGCAATTCTGCT\n+AAATCGGGTTGCCCTGCCAAAAGGCTGGCCGTTTTGCGCATTCAATAACA\n+CAAGCTAACGGTTTACAGCACATTCGGAAAGATCCAAAAGAATTTCTATT\n+TCGGCATTTTTTATGTATTATCGTCTAATTTTGGTATGTGTATTCATTCT\n+TTTGGCTGTCCGTTATTAAGCTGCTTTTCTTATTCACATATTCAATGGCG\n+CAGTACATAAAAAGAATGAACCGTGGTTTTCTTGCCCTCTCCATCTCCCT\n+CTACCACTTCCCCTCTCAACAACTATCTCACGCACTCTGTCCCTTCTCGT\n+CTCTGTCACCCTCTCTTTACCTACCTCACTCTGGCACACTCTCTCTACCT\n+ATCTCACTCTGTCACCTTCTTCTACCTAATTCTCTCTGTCGCGCTCGCTC\n+TCTCAACATGCCTTTCGCACCGTATCTCTTCGTTTCTCTGTATGCTTGCT\n+CTCTTAATTTAAGTTTCTCTTTCTTTGTGTTCAATATCTTTCGCGCTCGT\n+GACTCCTATTGACCGGACTCTGAGCGGTGCTCATTAAGAGTGGAGTTTTC\n+GATGATGGCGGGTGGCGCGAACGAGAATTTTTTACATAAAGGTAAGTTGC\n+CAATTCTTTTTTAAATGTGACATACAGCATGCATATTTTATTTATTGTAA\n+TTATATGTGAAAGAATAAAATTATATGTACTTTTATCTAATCTATTGCAT\n+CTATTTTTTCACAGGTAAACGAGTCACACGAGAAGTAAAACACAAACACA\n+AGGATCAAAATAAAATTCAGGTGAGTGAACGAACGTGTTGAAAGTAGTTA\n+ATAGTGCATGTCTATTTAAGTGTAAGAAACAAAAAAGACACAAATGGGCC\n+AATAATTCGTTTCTTTAATAGATAACTGCCTATATTATGTTCAAACTATG\n+CTAAAAAGACCCAAAAGGAAAACATAAAGTATATACCTTGCAAAATGAAT\n+AAAAAGAAATCATATATATTCATATACGTTTGACCGGTACCACCGGTCAT\n+ACATACATAAACATAAACACAAAAAGACTAGAATATAAATACCATATTTT\n+TGATTGGCTTAAAAATGGCACAAAAAAAAGATAAAAACTAGAGTGTCTAG\n+CTTTAAGTGACAATCGACTCGGAAAATGATCAAGAAATAAATGAAAAATT\n+TGTCTTGCGGCTTTTTGGTCGCAATTCTAAATCGGTTTGTATGTATGTCA\n+CTCTTCATGTATACAATTTGGTGGCTTTGTATTCCACAAAAGTCACAGTA\n+GTCACAAAAGTTTTTTTTACTGAAAATTACCATCAAGAGTCTATGGCCAA\n+ATCAGAATATTTTCACTGCGGTTTTTTATTTCAATTCTGCTAAATCGGGT\n+TTCCGTGCCAAAAAGCTTTTGCAGCCAACAACAATATTCAATTTTTTGGC\n+AAAAAATCGACAAAAAAATT\n' |
| b |
| diff -r 000000000000 -r ba819b65bef3 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon May 01 17:34:42 2017 -0400 |
| b |
| @@ -0,0 +1,61 @@ +<?xml version="1.0"?> +<tool_dependency> + <!-- Package trfBig --> + <package name="trfBig" version="1.0"> + <install version="1.0"> + <actions> + <action type="download_binary" target_directory="bin"> + <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/trfBig</url_template> + <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/trfBig</url_template> + </action> + <action type="chmod"> + <file mode="750">$INSTALL_DIR/bin/trfBig</file> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme>The tools downloaded by this dependency definition are free for academic use.</readme> + </package> + + <!-- Package trf --> + <!-- https://tandem.bu.edu/trf/downloads/trf407b.linux64 --> + <package name="trf" version="4.07b"> + <install version="1.0"> + <actions_group> + <actions architecture="x86_64" os="linux"> + <action type="download_by_url" target_directory="bin"> + https://tandem.bu.edu/trf/downloads/trf407b.linux64 + </action> + <action type="move_file" rename_to="trf"> + <source>trf407b.linux64</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="chmod"> + <file mode="750">$INSTALL_DIR/bin/trf</file> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + <actions architecture="x86_64" os="darwin"> + <action type="download_by_url" target_directory="bin"> + https://tandem.bu.edu/trf/downloads/trf407b.macos64 + </action> + <action type="move_file" rename_to="trf" os="darwin"> + <source>trf407b.macos64</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="chmod"> + <file mode="750">$INSTALL_DIR/bin/trf</file> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </actions_group> + </install> + <readme>The tools downloaded by this dependency definition are free for academic use.</readme> + </package> +</tool_dependency> \ No newline at end of file |
| b |
| diff -r 000000000000 -r ba819b65bef3 trfBig.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trfBig.xml Mon May 01 17:34:42 2017 -0400 |
| b |
| @@ -0,0 +1,26 @@ +<tool id="trfBig" name="TrfBig" version="0.1.0"> + <description>trfBig - Mask tandem repeats on a big sequence file</description> + <requirements> + <requirement type="package" version="4.07b">trf</requirement> + <!--<requirement type="package" version="324">ucsc-trfbig</requirement>--> + <requirement type="package" version="1.0">trfBig</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command> + trfBig -bedAt=$output $input /dev/null + </command> + <inputs> + <param format="fasta" name="input" type="data" /> + </inputs> + <outputs> + <data format="bed" name="output" /> + </outputs> + <help> + This will repeatedly run trf to mask tandem repeats in infile + and put masked results in outFile. inFile and outFile can be .fa + or .nib format. Outfile can be .bed as well. Sequence output is hard + masked, lowercase. + </help> +</tool> |