# HG changeset patch # User mvdbeek # Date 1430228336 14400 # Node ID c15a93753e7132b762de85756ca6cd15a924276d Uploaded diff -r 000000000000 -r c15a93753e71 get_reference_fasta.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_reference_fasta.xml Tue Apr 28 09:38:56 2015 -0400 @@ -0,0 +1,29 @@ + +Obtain reference genome sequence + + + + "$output" + ]]> + + + + + + + + + + + + + + + + diff -r 000000000000 -r c15a93753e71 test-data/EcR_USP_224.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/EcR_USP_224.fa Tue Apr 28 09:38:56 2015 -0400 @@ -0,0 +1,101 @@ +>3L:3245372,3251371 +AGGAGGCTATGTTTCTTAATGATGAACTGGTATATTATATTTTCGAAACTTTCATTTAAT +GTAAAAACACTGTTATTAGTAAATGGAATCTTCCATAACAGGGTCCACCCCAATCGATCA +TCCCACTCATTAGGTTTCTTCCTCGTCTGAGAGGACCAGAGGTCCCGAGGCTTGCGTTTT +TGCGGTGACTGTGGCGTCTGCTGGGTGTCAACATTTAGCCGCATGTTGTGCGGCTGCCAC +AACTGCAGTTCCCCAATTCTGGATAAAAAAAAAAAAACGCCGTCAAACAGAAGGGTGAAA +TTAACTTCGGAGTCGGACGAGGAGGAGTGCTTAGCACCCGCATCCAGGCACATGTGCTGT +TCTTCTCGACATGCGACATTCGTACAGTCGCCGAGTCAATCAGACCGGAAAATATGCACA +AATTCCAATGGCTTTTGTCATGTTGCAAGGCGATTGTGACTACATTTTTGCCATTTCTAT +TTCCCAAATAGCGGCTAAAACAGTTGTGGCCATTAACTTAGTGCTATGAATGTAGTTACT +GTTCTTGTGAATTGCTTAATTTCCCTTTCAATCATCTAAAATAAATAAATACAAATGAAT +GAACCAAAGTCATTACCCTGCCTAAAACACATTTTCTTCCCTTAGAACTTTGTACCCCTT +TTATATTTCGAATTGCAAATGGAAGGGTGAAATTAGCGGCAAGTGGAGCTATTTTCCGCG +CGGTGTATGGTTATCACAACGCTTATCTCACTACGCGATTGTCGGAACCTGTAAACGCGA +TTTTGTCAGCCAGGTTTTTTTGGCTGCCAGCACTTGACGTGTGTTAAATTAGCATTAAAC +AATAATTTTGTGCCTGTTTTTCTTTTTTTGGCTTTGCCGCTGTTGTTGTTGCTGTTACTG +TTGTGGTGAATGCAAAATAAATTGCGCATAAAGTTTAATCACTTTGACTTTGCACAACAC +ACACGCACGCACACACACTTGCAATGCCAAAAAATAAAAACGCACAACAAAAGATTCTCC +ACACACAGATACACAGATACTGAATACAATATCGGCAGCAGCAGCGCAAACCAAAACAAC +AACGACGAGCCCAGTGGACAGTGCAAAATAAGTATAAAAATAAATAAGAAAAATTAAAAA +AAAAGGAAATAAATAAAAAAATACACAAGGCGAAGGCGACGATGGCAACAGGCAGAGCGA +GCGGGATGCAAATAGAGTCAACAACCTCCAGTGCATTACTCACTTTTAAAGACCGTGTCT +GTCCTTCAACGAAAACTTTATCTCTGTCCCTCACTCGCTCGCTCTGCATCTGCATCTCAG +CTTTTGCTCCCTCTCTCTCTCGCTCGCTCTCACTCGAGCAGCCCGATTCGTTTTTTACTT +CTTATAATTAAACAATTTTGCAGCGGCACTCCCCCAGCGCCCCCATTTCGTACTCCCCCC +GCCGTCTTCATCTTTTTCCGGACAAACAGAACCCGAAAAAGTGATCTTGCTGCACGGAAA +GAAATCGAATCGTTGTCTAACAATAGAAATGCTGCTTTATAAGGCAACCAATTGAAGTCT +TTCGTTCTTCAAAACCTAATTCAAAGATTAACCACTTTTTTGCTATATCTATCCTTAAGC +TTTAAAATTCGAATAGTAATAGGATTTAACTCTATAGTAGTAGTATCTTATCATATTATC +AGTACGATTTTTCCCAAAGTGCCATTGTTTTTGGTCACTATGGTCTTGTTCTTGTTCCCG +GAGATTTGCACAAGTGTGCAGAAGACAGTCTTCTATCTCCACTTTATCGATGGGGCTTCG +GAAAGTTTGTCGATTCCGCTGCTGCGCATTTTGGCGAGATGCGAGATGAATAAACTGTTG +TACGCTTGCGTGACCTGTTCGCCATCTCGGTTGCTCCTCCTGCGCCCTCTTTTCCTCTCT +CTACCCCCCTCCCCCACGCAAAGGAAAGAGACGGAGCGATTGCCACATCCGCCCTGCATG +TTTGTGCGCTTTTTGTGCGACTAATGTCATTGACTGCAATTTGTTAGCAAAGTATTTCGA +CTGATAAACAAAATCTGCACGATGCCAATGAACCCGGCTCTCTAAAATTGCCATCCGAAA +GCCAAAACAACCCGAAATTGCAATTCGCGCCCCAATTGGAGAGCAACTAGGTAGGCGTGT +GTAACAGAGATAGCAATCGGGCCTTGCACTCACACTCCCTAAGGAGCAGAGGTGGATTCT +AACGGGGATTTGACGGAACGCGAATTCTTTAGCATTCTATATCTGCACCTTATAAGAATT +TCCACTGAGTTCTAAGTTGAGATTTCATAATATTTAGTATTTTAACTATGTTTTTTCGTA +TAAGTTTTGTTATTACTCTGCTATGACTTCCATAACCCCTTTTTAGAAGTGCTTTTCCTT +ATCCGCCTCTGCACATGAGCACAGGTTGGCAATGCCATAAACAAAGAATTCCTTTTGTTT +GTTGATTCGATTTTTGTTCTGCGATCTTTTTATTTCTTTGCAAATTGTATTTTTATTTTT +AAATAAACAAGCCGAGTTCATTGCATTCGCCAGAATAAGAATATAACAAATACGGCACGA +AAAGCACTCGACAACCGACAAAAGGCGCAGAAAAACAGGAACGTCGACTGACATACATGG +CGTATAATTAACGGCTGCGCGTGTAGAGAGAGTTCAAGTTACTTTATCAATTCTTTCTTT +TTCGGGACCTAACAATACTCATACTTGCACTTAAGTAGGCGGAGTGAAAGCCAAGTCATA +ATTTCGACGATGCGTATACATATATAGAATCAATCAACTGATTAATTGCAGCTGTGCAAC +GCTTGAGTTTTTGCCTCAGCCTTTCGTCTGGTGACATAGTTTACTCGATTAATTATGGTA +AGTAATAAGGGTTTAAAATAATTGAAAACCCCAGCACTTGCGTGTATTATATATAACGAT +GATTTAACAGCACCTCCTTTATAAATAAAACCAATCCCTTCAAGTGCGAACAGCTATGTT +TTCCGCTCATCTGGCGCATTTATCAGATGGTGCCATATTTCCTCGGAGAAGAAGGCATTG +AATGTCAGTGGTGTTCGGATTACACTAAAGTCGGTCAATAACTTCGGACCCCTGCACAAA +GCGTTTAAGTGACCACAAGTGATCGAGATGTTCCTCTTGTTGTTTACCCCCTTGCCAACT +GATCTTAAGTTTGGGATGCCACGCTAGTTTAGTTGACCGGTTTAATGACTCGAACTTAAT +TTGCGCCCTCGGAGAGAGGAAAGTAGCCAGCAAAAAATGCAAGCCGAAAAATATGCGAAA +CAACCAGGCAGACAACACCCAACGGCAAAAACTCGGCCTGGAGAGAAAGAGGCAGTGGCA +GCGACGCGTCTGGGGGCTTACAATGGCGGTCGCAACACTAGTGGCGCTTGTAAATAGAGA +CATAACGAAAAGGTATTAAAAATGATGCGGCAAAAGAAATAACTGCACTATTTTCCATAA +AAATATTTTGAAAAATAAACTGTTGCGCCGTTTTTAGAGATCTTAAAAACCTCTTTACGT +CAACTTTGATAACTAATTGAGTTCCTTTGCATAGTTATGATTTTTAAAAATAACAATTTA +AGATACATGATATTCCCTACATGAACAATTAGTGGTTTATAATAAATAAGCAACCTAATG +CGTAAGATCCCACAATCTTGACCGCTACTGTGAAAAGGGGGGGATCTGCGTGAGTGTGCG +TGTATGTGGGGAGAGGGCTGCAGTGGGCGGGGCAGGCTGCAGGAAGAGCCCCCAGGCGAG +CGTGTGTATGTGAGTGGGTCGCCAAAACAGACAAAAAACGAGGAGTGCATACGAGCAGAA +GCAGCAGTGCTGCCCCAAAAGAACGATGCTCGAACCGAAAGTAACTCATATTCGCGGCTG +CGAGAGTGTGTGCGTGTGCGGCGACGGATCAGGCAAATATATAAAGCGGCGATCGGGCAA +TGCAAACTGCTCATTCCGTCGCCGTTCGTTCCGTTCGCTTTACTTTTCGTACTTTTCTCG +CATATTAAAAAGTCAAACAAAATAATAAAATGAAGCGATCGCACACATACTCACGCACAT +ACGTGTATATGTTCGTACATATATATATGTACATATGCATACATATATATGCACGCAATG +GCCGCCATTGACGCCGACTGCGCTGCCGACTGCGCTGGCGAGAGTATAAAAGCATAAAAT +CACTTCGTACTCGGGTTTATTAAAACCAAAACTGTGCAAGTGTCAAGATCGGTTAGCAGC +AGCAAAAAGATAAATAAGAAATAGCCAAGGACCCATAAAATAAATAATCTCAATACCAAA +AAGTTCTAGTGAAATTCACAATTCTGACTTGGAAAGTGAAAGTTTGGCCATTAAACGTAC +GATTAAAATCCACAACAGCACGATCAAAAATAGTATCAAGCAATTAGCGCAGAAAAAGTA +ACAAAAAAAATTTTAAAAAACAGGAACGCGACGTGCCCGCAAAAGCGAAAAAAAATTAAA +ATCGAAAGTGTTCTACTGACATGGATTACTTTTTGCCGCCCAAACTACAAACACAACAAA +ACGCGCAGAGAAACTAGCACTACTTTTTTCTATTCACCCATTCGGAGAGTGAGAAGAATC +GGAGAGAAGGAAAGAGAGCAAAGGCCGGTCCGAAATAGAAAGCACTACACTGGAAAATCT +GTTAATAAGAATGCAATGAAAGTAATACGAAACACAGATATATTTAGCTTATATTACTCT +TAAAACTCTAGAAAAATCTAGATCGGTTAATATAACAATTTTAAAATAGCTTAGTTGGCA +TCGATGTTACGGAAAAAATTTTTCCAGTTGTACTTGAAAGGCAGAAATATTTCGAGATTT +AGATTTATGAGTCTTCCTAAAGAAATTAAATTGGATAGAAAATGTCTTTTAGATATAGAA +TACAGGGTGATGCCTAATCCATTAAAATCGAGCAATCTAAAAAGTGTCATACCAGTTAGA +TTGGGTGTAACCAACGCAACGTTCTCACTGTGTAGATAGCGATCTCTTCTATTCGGCGGT +GTACGTGCACTTGGCCATTTGTCTCTCCATTCTCCATTTTTCGCGCCTCGCTCTCAATTC +TCTGCGCTCAAATCCTCTAGCAATTCTAATTCGTATTCTCGCCGCCTCGCTTTGAACTTG +AACTTTAAATGCACAAACCATAATCGTGTATGTTATGTTGTTGCTGGCCGAGGGCGTGCT +CTCGCACTCTGGCAAACATGGGCTCTACGAGTTTGCTATATATACGCAGCGCAATCAGTT +GCGAGGCAGCACTCGTTCCATGTGGGCGCTCGACAATCGCCCGCTGATCAGTTTTCGACT +GGCTTGCAATTAATTCGGCTCTTGACGAGCCCCAAAAGTGAAAGTCGCGAGTGAAAGACG +TGGCAGTTTTATATTAAAGAAAAATACGAAAACGGGCAGCAGATCAAACATGAACAGTAC +GCAAAACACGAAATGCGAAACGGCGGCAACAAGTTAATAAATTAAGACGGCAAACGAAAA +AATCCAGATTCCGAGCACTGCAAAGAAAGTGGCACAAATGCTTTGCTTTTATCGTAGGAA +ATTCGCAAAAAATGTACAAATAAAACGAAAGAAAAGTTGCCACTATCAAATCCCACCGTT +CTTTAACTATAGTTTCCTTCTAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATTCGAAA +GCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGCGAACAATCAGCGAAAACG +GAATCGATTACAGTTTTGGAGATCGTGAGAGGAGGAGAAGAGGCGACTGCTTGATAAGCC +CGGACCCTCCAGCGATCTCCAATCAATATTACTTTCCACCTACATATCTCCCCCTTTCAG +CTGGTTTAATTTTGGATTCCCCCATCTGGCTGGCCTATTTTCGCCTGGCCTGCGTTATTT +ATTAGTTAATAAACCATTAATATATACTTGAATAAAAAGGCGTTTCTCTGATTTTTGATG \ No newline at end of file diff -r 000000000000 -r c15a93753e71 test-data/all_fasta.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Tue Apr 28 09:38:56 2015 -0400 @@ -0,0 +1,1 @@ +EcR_USP_224.fa EcR_USP_224.fa EcR_USP_224.fa ${__HERE__}/EcR_USP_224.fa diff -r 000000000000 -r c15a93753e71 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Apr 28 09:38:56 2015 -0400 @@ -0,0 +1,7 @@ + + + + value, dbkey, name, path + +
+
diff -r 000000000000 -r c15a93753e71 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue Apr 28 09:38:56 2015 -0400 @@ -0,0 +1,6 @@ + + + value, dbkey, name, path + +
+