| Next changeset 1:6eaefb5f755a (2014-11-17) |
|
Commit message:
Imported from capsule None |
|
added:
test-data/tophat_in1.fasta test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger test-data/tophat_out1h.bam test-data/tophat_out1j.bed test-data/tophat_out2h.bam test-data/tophat_out2j.bed test-data/tophat_out3d.bed test-data/tophat_out3h.bam test-data/tophat_out3i.bed test-data/tophat_out3j.bed test-data/tophat_out4h.bam test-data/tophat_out4j.bed tool-data/bowtie_indices.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml tophat_macros.xml tophat_wrapper.py tophat_wrapper.xml |
| b |
| diff -r 000000000000 -r 1030acbecce6 test-data/tophat_in1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_in1.fasta Mon Jan 27 09:25:27 2014 -0500 |
| b |
| @@ -0,0 +1,14 @@ +>test_chromosome +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +ACTACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCC +ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC +AGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCT +ACGTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCC +GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG +ACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT +GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG +TTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
| b |
| diff -r 000000000000 -r 1030acbecce6 test-data/tophat_in2.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_in2.fastqsanger Mon Jan 27 09:25:27 2014 -0500 |
| b |
| b'@@ -0,0 +1,400 @@\n+@test_mRNA_150_290_0/1\n+TCCTAAAAAGTCCGCCTCGGTCTCAGTCTCAAGTAGAAAAAGTCCCGTTGGCGATCCGTCTACGTCCGAGTAAGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_8_197_1/1\n+TCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGACACTACGGGGATGGCGACTAGGACTACGGACGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_82_255_2/1\n+GAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAATATAGTAAAGTAATAGTGGCGTATCGCAAGCTCGACG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_96_238_3/1\n+GATCCGTCTACGTCCGCGTAAGATAATAAAGTACTAGTAGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_72_258_4/1\n+GTAGAAAAAGTCCCGTTGCCCATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_107_286_5/1\n+AAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_122_299_6/1\n+CAAGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGCTCCGTCTACGTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_58_234_7/1\n+AGTCTACGTCCGAGTCAGATAATAAACTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_57_231_8/1\n+GGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCACCGACTGGACTATTTAGGACGATCGGACTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_8_155_9/1\n+TACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTACAGTCGCTGCATCTGACGCTCGAAGTCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_51_237_a/1\n+ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_89_230_b/1\n+TACGTCCGAGTGAGTTAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_105_276_c/1\n+CCTCGATCCCAGTCTCAAGTAGAAAAAGCCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_111_268_d/1\n+CCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAATAATAGTGGCGTAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_151_286_e/1\n+ACGTATTTGGCGCGCGGCCGTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_118_297_f/1\n+AGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_16_194_10/1\n+TCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_28_188_11/1\n+TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGAACGGACTTAGAGCGTCAGATGCAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_36_218_12/1\n+GAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGCCTTAGAGCGTCAGATGCAGCGACTGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_105_266_13/1\n+AGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGGATCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_51_248_14/1\n+ACTACGGGGATGACGACGAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGAACTTTTTAGGACGATC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_89_245_15/1\n+AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mR'..b'IIIIIIIIIIIIIII\n+@test_mRNA_33_223_4e/1\n+ACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_172_294_4f/1\n+ACGGATGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTCCTCGGACGTAGACGGATCGCCAACGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_88_257_50/1\n+TAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_3_187_51/1\n+TACTATTTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_9_179_52/1\n+TCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATGGTCCAGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_85_268_53/1\n+TTAGTGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_75_204_54/1\n+ACGGACGGACTTCGAGCCTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_41_236_55/1\n+AGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_56_183_56/1\n+GGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTGGGACGATCGGACT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_87_250_57/1\n+AGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_82_271_58/1\n+GACTTAGAGCGTCAGTTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_6_182_59/1\n+TATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAGTACGGGGATGACGACTAGGACTACGGAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_53_272_5a/1\n+GATCCCAGTGTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_114_277_5b/1\n+GCCTCGATCCCAGTCTCAAGCAGAAAAAGTCCCGTTGCCGTTCCGTCTACCTCCGAGTAAGATAATAAAGTAATA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_39_219_5c/1\n+CTAGGACGTCCCACTATGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGGCTGGACTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_4_191_5d/1\n+CAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGTGTCCTACTGCCCTACTCAGTCCGATCGTCCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_73_259_5e/1\n+CTACGGACGGACTTAGAGCGTCAGATGCTGCGACTGGACTATTTGGGACGATCGGACTGAGGAGGGCAGTAGGAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_87_279_5f/1\n+CCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_125_293_60/1\n+CCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_111_297_61/1\n+AGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCGGATCCGTCTACGTCCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_22_173_62/1\n+AGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_116_295_63/1\n+TCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n' |
| b |
| diff -r 000000000000 -r 1030acbecce6 test-data/tophat_in3.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_in3.fastqsanger Mon Jan 27 09:25:27 2014 -0500 |
| b |
| b'@@ -0,0 +1,400 @@\n+@test_mRNA_150_290_0/2\n+TACGTATTTGTCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATCCGCCACTATTACTTTATTATCTTACTCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_8_197_1/2\n+GTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_82_255_2/2\n+GACTTAGAGCGTCAGATGCAGCGACTGGACTTTTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_96_238_3/2\n+GATGCAGCGACTGGACTATTTAGGACGATCGGACGGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGACC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_72_258_4/2\n+ACTACGGACGGACTTAGAGCGTCAGATGCAGCAACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_107_286_5/2\n+TGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGCATTTGGCGCGCGGCCCTACGGCTGAGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_122_299_6/2\n+GATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_58_234_7/2\n+GGATGACGCCTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_57_231_8/2\n+CTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCCTAGGGCCGCGCGCCAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_8_155_9/2\n+TGTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_51_237_a/2\n+ATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_89_230_b/2\n+AGCGTCAGGTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_105_276_c/2\n+ACTGGACTATTTAGGACGATCGGACTGAGGAAGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_111_268_d/2\n+CTATTTAAGACGTTCCGCCTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_151_286_e/2\n+AAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGATAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_118_297_f/2\n+GGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_16_194_10/2\n+GACTGGATGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACGGACGGACTTAAAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_28_188_11/2\n+GCTCGACGCTCAGCCGTAGGGCCTCGCGCCAAATACGAAGCGTCCTACTGCCTTCCTCAGTCCGATCGTCCTAAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_36_218_12/2\n+AGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_105_266_13/2\n+ACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_51_248_14/2\n+TCCCGTTGCCGTTCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_89_245_15/2\n+CGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAGAGAAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mR'..b'IIIIIIIIIIIIIII\n+@test_mRNA_33_223_4e/2\n+GAGTTAGATAATAAAGTAATAGTGGCTTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACCTAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_172_294_4f/2\n+CCCGTCCTAAAACGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGCTGCCGACCCGTCTACGTCCGAGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_88_257_50/2\n+GAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_3_187_51/2\n+CTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_9_179_52/2\n+CTGACTAGACTGGAGGCGCTCGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_85_268_53/2\n+CCAGTCTCAAGTAGAAAAAGTCCCGTTGACGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_75_204_54/2\n+TCGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_41_236_55/2\n+TCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_56_183_56/2\n+ACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_87_250_57/2\n+AGAGCGTCAGATGCAGAGACTGGACTATTTAGGACGATCGGACTGAGGAGTGCAGTAGGACGCTACGTATTTGGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_82_271_58/2\n+ATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATGCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_6_182_59/2\n+CGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_53_272_5a/2\n+TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_114_277_5b/2\n+TTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGCCTGAGCGTCGAGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_39_219_5c/2\n+AAGATAATAAAGTAATAGTGGCGTATCGCAAGCTGGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_4_191_5d/2\n+ACTATCTGACGAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTACCATTACGCGGATGACGACTAGGACTACGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_73_259_5e/2\n+AGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATACAGTAATAGTGGCGTATCGCAAGCTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_87_279_5f/2\n+AGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACCGAGGAGGGCAGTAGGACGCTACGTATTTGGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_125_293_60/2\n+CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCTTCGAGGTTGCGATACGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_111_297_61/2\n+CTATTTAGGACGATCGGACTGGGGAGGGCAGTAGGACGCTACGGATTTGGCGCGCGGCCCTACGGCTGAGCGTCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_22_173_62/2\n+GTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTCCAGTCGCTGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_116_295_63/2\n+TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n' |
| b |
| diff -r 000000000000 -r 1030acbecce6 test-data/tophat_out1h.bam |
| b |
| Binary file test-data/tophat_out1h.bam has changed |
| b |
| diff -r 000000000000 -r 1030acbecce6 test-data/tophat_out1j.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_out1j.bed Mon Jan 27 09:25:27 2014 -0500 |
| b |
| @@ -0,0 +1,3 @@ +track name=junctions description="TopHat junctions" +test_chromosome 180 400 JUNC00000001 23 + 180 400 255,0,0 2 70,50 0,170 +test_chromosome 350 550 JUNC00000002 24 + 350 550 255,0,0 2 50,50 0,150 |
| b |
| diff -r 000000000000 -r 1030acbecce6 test-data/tophat_out2h.bam |
| b |
| Binary file test-data/tophat_out2h.bam has changed |
| b |
| diff -r 000000000000 -r 1030acbecce6 test-data/tophat_out2j.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_out2j.bed Mon Jan 27 09:25:27 2014 -0500 |
| b |
| @@ -0,0 +1,3 @@ +track name=junctions description="TopHat junctions" +test_chromosome 179 400 JUNC00000001 38 + 179 400 255,0,0 2 71,50 0,171 +test_chromosome 350 549 JUNC00000002 30 + 350 549 255,0,0 2 50,49 0,150 |
| b |
| diff -r 000000000000 -r 1030acbecce6 test-data/tophat_out3d.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_out3d.bed Mon Jan 27 09:25:27 2014 -0500 |
| b |
| @@ -0,0 +1,1 @@ +track name=deletions description="TopHat deletions" |
| b |
| diff -r 000000000000 -r 1030acbecce6 test-data/tophat_out3h.bam |
| b |
| Binary file test-data/tophat_out3h.bam has changed |
| b |
| diff -r 000000000000 -r 1030acbecce6 test-data/tophat_out3i.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_out3i.bed Mon Jan 27 09:25:27 2014 -0500 |
| b |
| @@ -0,0 +1,1 @@ +track name=insertions description="TopHat insertions" |
| b |
| diff -r 000000000000 -r 1030acbecce6 test-data/tophat_out3j.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_out3j.bed Mon Jan 27 09:25:27 2014 -0500 |
| b |
| @@ -0,0 +1,3 @@ +track name=junctions description="TopHat junctions" +test_chromosome 180 400 JUNC00000001 23 + 180 400 255,0,0 2 70,50 0,170 +test_chromosome 350 550 JUNC00000002 24 + 350 550 255,0,0 2 50,50 0,150 |
| b |
| diff -r 000000000000 -r 1030acbecce6 test-data/tophat_out4h.bam |
| b |
| Binary file test-data/tophat_out4h.bam has changed |
| b |
| diff -r 000000000000 -r 1030acbecce6 test-data/tophat_out4j.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_out4j.bed Mon Jan 27 09:25:27 2014 -0500 |
| b |
| @@ -0,0 +1,3 @@ +track name=junctions description="TopHat junctions" +test_chromosome 179 400 JUNC00000001 38 + 179 400 255,0,0 2 71,50 0,171 +test_chromosome 350 549 JUNC00000002 30 + 350 549 255,0,0 2 50,49 0,150 |
| b |
| diff -r 000000000000 -r 1030acbecce6 tool-data/bowtie_indices.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/bowtie_indices.loc.sample Mon Jan 27 09:25:27 2014 -0500 |
| b |
| @@ -0,0 +1,37 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Bowtie indexed sequences data files. You will +#need to create these data files and then create a bowtie_indices.loc +#file similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bowtie_indices.loc +#file has this format (longer white space characters are TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg18 indexed stored in +#/depot/data2/galaxy/bowtie/hg18/, +#then the bowtie_indices.loc entry would look like this: +# +#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18 +# +#and your /depot/data2/galaxy/bowtie/hg18/ directory +#would contain hg18.*.ebwt files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt +#...etc... +# +#Your bowtie_indices.loc file should include an entry per line for each +#index set you have stored. The "file" in the path does not actually +#exist, but it is the prefix for the actual index files. For example: +# +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon +#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full +#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 +#...etc... +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. That is why the +#hg19 entry above looks odd. New genomes can be better-looking. +# |
| b |
| diff -r 000000000000 -r 1030acbecce6 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Jan 27 09:25:27 2014 -0500 |
| b |
| @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of indexes in the Bowtie mapper format for TopHat to use --> + <table name="tophat_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bowtie_indices.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r 1030acbecce6 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jan 27 09:25:27 2014 -0500 |
| b |
| @@ -0,0 +1,12 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="bowtie" version="0.12.7"> + <repository changeset_revision="028d22e7b70f" name="package_bowtie_0_12_7" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="samtools" version="0.1.18"> + <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="tophat" version="1.4.0"> + <repository changeset_revision="0fea0c8cc6cf" name="package_tophat_1_4_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |
| b |
| diff -r 000000000000 -r 1030acbecce6 tophat_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tophat_macros.xml Mon Jan 27 09:25:27 2014 -0500 |
| [ |
| @@ -0,0 +1,72 @@ +<macros> + <macro name="refGenomeSourceConditional"> + <conditional name="refGenomeSource"> + <param name="genomeSource" type="select" label="Use a built in reference genome or own from your history" help="Built-ins genomes were created using default options"> + <option value="indexed" selected="True">Use a built-in genome</option> + <option value="history">Use a genome from history</option> + </param> + <when value="indexed"> + <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> + <yield /> + </param> + </when> + <when value="history"> + <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" /> + </when> <!-- history --> + </conditional> <!-- refGenomeSource --> + </macro> + <macro name="indel_searchConditional"> + <conditional name="indel_search"> + <param name="allow_indel_search" type="select" label="Allow indel search"> + <option value="Yes">Yes</option> + <option value="No">No</option> + </param> + <when value="No"/> + <when value="Yes"> + <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." /> + <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." /> + </when> + </conditional> + </macro> + <macro name="own_junctionsConditional"> + <conditional name="own_junctions"> + <param name="use_junctions" type="select" label="Use Own Junctions"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="Yes"> + <conditional name="gene_model_ann"> + <param name="use_annotations" type="select" label="Use Gene Annotation Model"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="No" /> + <when value="Yes"> + <param format="gtf,gff3" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/> + </when> + </conditional> + <expand macro="raw_juncsConditional" /> + <expand macro="no_novel_juncsParam" /> + </when> + <when value="No" /> + </conditional> <!-- /own_junctions --> + </macro> + <macro name="raw_juncsConditional"> + <conditional name="raw_juncs"> + <param name="use_juncs" type="select" label="Use Raw Junctions"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="No" /> + <when value="Yes"> + <param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/> + </when> + </conditional> + </macro> + <macro name="no_novel_juncsParam"> + <param name="no_novel_juncs" type="select" label="Only look for supplied junctions"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + </macro> +</macros> |
| b |
| diff -r 000000000000 -r 1030acbecce6 tophat_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tophat_wrapper.py Mon Jan 27 09:25:27 2014 -0500 |
| b |
| b'@@ -0,0 +1,238 @@\n+#!/usr/bin/env python\n+\n+import optparse, os, shutil, subprocess, sys, tempfile, fileinput\n+\n+def stop_err( msg ):\n+ sys.stderr.write( "%s\\n" % msg )\n+ sys.exit()\n+\n+def __main__():\n+ #Parse Command Line\n+ parser = optparse.OptionParser()\n+ parser.add_option( \'-p\', \'--num-threads\', dest=\'num_threads\', help=\'Use this many threads to align reads. The default is 1.\' )\n+ parser.add_option( \'-C\', \'--color-space\', dest=\'color_space\', action=\'store_true\', help=\'This indicates color-space data\' )\n+ parser.add_option( \'-J\', \'--junctions-output\', dest=\'junctions_output_file\', help=\'Junctions output file; formate is BED.\' )\n+ parser.add_option( \'-H\', \'--hits-output\', dest=\'accepted_hits_output_file\', help=\'Accepted hits output file; formate is BAM.\' )\n+ parser.add_option( \'\', \'--own-file\', dest=\'own_file\', help=\'\' )\n+ parser.add_option( \'-D\', \'--indexes-path\', dest=\'index_path\', help=\'Indexes directory; location of .ebwt and .fa files.\' )\n+ parser.add_option( \'-r\', \'--mate-inner-dist\', dest=\'mate_inner_dist\', help=\'This is the expected (mean) inner distance between mate pairs. \\\n+ For, example, for paired end runs with fragments selected at 300bp, \\\n+ where each end is 50bp, you should set -r to be 200. There is no default, \\\n+ and this parameter is required for paired end runs.\')\n+ parser.add_option( \'\', \'--mate-std-dev\', dest=\'mate_std_dev\', help=\'Standard deviation of distribution on inner distances between male pairs.\' )\n+ parser.add_option( \'-a\', \'--min-anchor-length\', dest=\'min_anchor_length\', \n+ help=\'The "anchor length". TopHat will report junctions spanned by reads with at least this many bases on each side of the junction.\' )\n+ parser.add_option( \'-m\', \'--splice-mismatches\', dest=\'splice_mismatches\', help=\'The maximum number of mismatches that can appear in the anchor region of a spliced alignment.\' )\n+ parser.add_option( \'-i\', \'--min-intron-length\', dest=\'min_intron_length\', \n+ help=\'The minimum intron length. TopHat will ignore donor/acceptor pairs closer than this many bases apart.\' )\n+ parser.add_option( \'-I\', \'--max-intron-length\', dest=\'max_intron_length\', \n+ help=\'The maximum intron length. When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read.\' )\n+ parser.add_option( \'-g\', \'--max_multihits\', dest=\'max_multihits\', help=\'Maximum number of alignments to be allowed\' )\n+ parser.add_option( \'\', \'--initial-read-mismatches\', dest=\'initial_read_mismatches\', help=\'Number of mismatches allowed in the initial read mapping\' )\n+ parser.add_option( \'\', \'--seg-mismatches\', dest=\'seg_mismatches\', help=\'Number of mismatches allowed in each segment alignment for reads mapped independently\' )\n+ parser.add_option( \'\', \'--seg-length\', dest=\'seg_length\', help=\'Minimum length of read segments\' )\n+ parser.add_option( \'\', \'--library-type\', dest=\'library_type\', help=\'TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol.\' )\n+ parser.add_option( \'\', \'--allow-indels\', action="store_true", help=\'Allow indel search. Indel search is disabled by default.(Not used since version 1.3.0)\' )\n+ parser.add_option( \'\', \'--max-insertion-length\', dest=\'max_insertion_length\', help=\'The maximum insertion length. The default is 3.\' )\n+ parser.add_option( \'\', \'--max-deletion-length\', dest=\'max_deletion_length\', help=\'The maximum deletion length. The default is 3.\' )\n+\n+ # Options for supplying own juncti'..b'f options.raw_juncs:\n+ opts += \' -j %s\' % options.raw_juncs\n+ if options.no_novel_juncs:\n+ opts += \' --no-novel-juncs\'\n+ if options.library_type:\n+ opts += \' --library-type %s\' % options.library_type\n+ if options.no_novel_indels:\n+ opts += \' --no-novel-indels\'\n+ else:\n+ if options.max_insertion_length:\n+ opts += \' --max-insertion-length %i\' % int( options.max_insertion_length )\n+ if options.max_deletion_length:\n+ opts += \' --max-deletion-length %i\' % int( options.max_deletion_length )\n+ # Max options do not work for Tophat v1.2.0, despite documentation to the contrary. (Fixed in version 1.3.1)\n+ # need to warn user of this fact\n+ #sys.stdout.write( "Max insertion length and max deletion length options don\'t work in Tophat v1.2.0\\n" )\n+\n+ # Search type options.\n+ if options.coverage_search:\n+ opts += \' --coverage-search --min-coverage-intron %s --max-coverage-intron %s\' % ( options.min_coverage_intron, options.max_coverage_intron )\n+ else:\n+ opts += \' --no-coverage-search\'\n+ if options.closure_search:\n+ opts += \' --closure-search --min-closure-exon %s --min-closure-intron %s --max-closure-intron %s\' % ( options.min_closure_exon, options.min_closure_intron, options.max_closure_intron ) \n+ else:\n+ opts += \' --no-closure-search\'\n+ if options.microexon_search:\n+ opts += \' --microexon-search\'\n+ if options.single_paired == \'paired\':\n+ opts += \' --mate-std-dev %s\' % options.mate_std_dev\n+ if options.initial_read_mismatches:\n+ opts += \' --initial-read-mismatches %d\' % int( options.initial_read_mismatches )\n+ if options.seg_mismatches:\n+ opts += \' --segment-mismatches %d\' % int( options.seg_mismatches )\n+ if options.seg_length:\n+ opts += \' --segment-length %d\' % int( options.seg_length )\n+ if options.min_segment_intron:\n+ opts += \' --min-segment-intron %d\' % int( options.min_segment_intron )\n+ if options.max_segment_intron:\n+ opts += \' --max-segment-intron %d\' % int( options.max_segment_intron )\n+ cmd = cmd % ( opts, index_path, reads )\n+ except Exception, e:\n+ # Clean up temp dirs\n+ if os.path.exists( tmp_index_dir ):\n+ shutil.rmtree( tmp_index_dir )\n+ stop_err( \'Something is wrong with the alignment parameters and the alignment could not be run\\n\' + str( e ) )\n+ #print cmd\n+\n+ # Run\n+ try:\n+ tmp_out = tempfile.NamedTemporaryFile().name\n+ tmp_stdout = open( tmp_out, \'wb\' )\n+ tmp_err = tempfile.NamedTemporaryFile().name\n+ tmp_stderr = open( tmp_err, \'wb\' )\n+ print cmd\n+ proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr )\n+ returncode = proc.wait()\n+ tmp_stderr.close()\n+ # get stderr, allowing for case where it\'s very large\n+ tmp_stderr = open( tmp_err, \'rb\' )\n+ stderr = \'\'\n+ buffsize = 1048576\n+ try:\n+ while True:\n+ stderr += tmp_stderr.read( buffsize )\n+ if not stderr or len( stderr ) % buffsize != 0:\n+ break\n+ except OverflowError:\n+ pass\n+ tmp_stdout.close()\n+ tmp_stderr.close()\n+ if returncode != 0:\n+ raise Exception, stderr\n+ \n+ # TODO: look for errors in program output.\n+ except Exception, e:\n+ stop_err( \'Error in tophat:\\n\' + str( e ) ) \n+\n+ # Clean up temp dirs\n+ if os.path.exists( tmp_index_dir ):\n+ shutil.rmtree( tmp_index_dir )\n+\n+if __name__=="__main__": __main__()\n' |
| b |
| diff -r 000000000000 -r 1030acbecce6 tophat_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tophat_wrapper.xml Mon Jan 27 09:25:27 2014 -0500 |
| [ |
| b'@@ -0,0 +1,563 @@\n+<tool id="tophat" name="Tophat for Illumina" version="1.5.0">\n+ <!-- Wrapper compatible with Tophat versions 1.3.0 to 1.4.1 -->\n+ <description>Find splice junctions using RNA-seq data</description>\n+ <version_command>tophat --version</version_command>\n+ <requirements>\n+ <requirement type="package" version="0.1.18">samtools</requirement>\n+ <requirement type="package" version="0.12.7">bowtie</requirement>\n+ <requirement type="package" version="1.4.0">tophat</requirement>\n+ </requirements>\n+ <command interpreter="python">\n+ tophat_wrapper.py\n+ ## Change this to accommodate the number of threads you have available.\n+ --num-threads="\\${GALAXY_SLOTS:-4}"\n+ ## Provide outputs.\n+ --junctions-output=$junctions\n+ --hits-output=$accepted_hits\n+\n+ ## Handle reference file.\n+ #if $refGenomeSource.genomeSource == "history":\n+ --own-file=$refGenomeSource.ownFile\n+ #else:\n+ --indexes-path="${refGenomeSource.index.fields.path}"\n+ #end if\n+\n+ ## Are reads single-end or paired?\n+ --single-paired=$singlePaired.sPaired\n+\n+ ## First input file always required.\n+ --input1=$input1\n+\n+ ## Set params based on whether reads are single-end or paired.\n+ #if $singlePaired.sPaired == "single":\n+ --settings=$singlePaired.sParams.sSettingsType\n+ #if $singlePaired.sParams.sSettingsType == "full":\n+ -a $singlePaired.sParams.anchor_length\n+ -m $singlePaired.sParams.splice_mismatches\n+ -i $singlePaired.sParams.min_intron_length\n+ -I $singlePaired.sParams.max_intron_length\n+ -g $singlePaired.sParams.max_multihits\n+ --min-segment-intron $singlePaired.sParams.min_segment_intron\n+ --max-segment-intron $singlePaired.sParams.max_segment_intron\n+ --initial-read-mismatches=$singlePaired.sParams.initial_read_mismatches\n+ --seg-mismatches=$singlePaired.sParams.seg_mismatches\n+ --seg-length=$singlePaired.sParams.seg_length\n+ --library-type=$singlePaired.sParams.library_type\n+ \n+ ## Indel search.\n+ #if $singlePaired.sParams.indel_search.allow_indel_search == "Yes":\n+ ## --allow-indels\n+ --max-insertion-length $singlePaired.sParams.indel_search.max_insertion_length\n+ --max-deletion-length $singlePaired.sParams.indel_search.max_deletion_length\n+ #else:\n+ --no-novel-indels\n+ #end if\n+\n+ ## Supplying junctions parameters.\n+ #if $singlePaired.sParams.own_junctions.use_junctions == "Yes":\n+ #if $singlePaired.sParams.own_junctions.gene_model_ann.use_annotations == "Yes":\n+ -G $singlePaired.sParams.own_junctions.gene_model_ann.gene_annotation_model\n+ #end if\n+ #if $singlePaired.sParams.own_junctions.raw_juncs.use_juncs == "Yes":\n+ -j $singlePaired.sParams.own_junctions.raw_juncs.raw_juncs\n+ #end if\n+ ## TODO: No idea why a string cast is necessary, but it is:\n+ #if str($singlePaired.sParams.own_junctions.no_novel_juncs) == "Yes":\n+ --no-novel-juncs\n+ #end if\n+ #end if\n+\n+ #if $singlePaired.sParams.closure_search.use_search == "Yes":\n+ --closure-search\n+ --min-closure-exon $singlePaired.sParams.closure_search.min_closure_exon\n+ --'..b' The maximum number of mismatches that may appear in the "anchor" region of a spliced alignment. The default is 0.\n+ -i/--min-intron-length INT The minimum intron length. TopHat will ignore donor/acceptor pairs closer than this many bases apart. The default is 70.\n+ -I/--max-intron-length INT The maximum intron length. When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read. The default is 500000.\n+ -g/--max-multihits INT Instructs TopHat to allow up to this many alignments to the reference for a given read, and suppresses all alignments for reads with more than this many \n+ alignments. The default is 40.\n+ -G/--GTF [GTF 2.2 file] Supply TopHat with a list of gene model annotations. TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping.\n+ -j/--raw-juncs [juncs file] Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-], left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive.\n+ -no-novel-juncs Only look for junctions indicated in the supplied GFF file. (ignored without -G)\n+ --no-closure-search Disables the mate pair closure-based search for junctions. Currently, has no effect - closure search is off by default.\n+ --closure-search Enables the mate pair closure-based search for junctions. Closure-based search should only be used when the expected inner distance between mates is small (about or less than 50bp)\n+ --no-coverage-search Disables the coverage based search for junctions.\n+ --coverage-search Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity.\n+ --microexon-search With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.\n+ --butterfly-search TopHat will use a slower but potentially more sensitive algorithm to find junctions in addition to its standard search. Consider using this if you expect that your experiment produced a lot of reads from pre-mRNA, that fall within the introns of your transcripts.\n+ --segment-mismatches Read segments are mapped independently, allowing up to this many mismatches in each segment alignment. The default is 2.\n+ --segment-length Each read is cut up into segments, each at least this long. These segments are mapped independently. The default is 25.\n+ --min-closure-exon During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50.\n+ --min-closure-intron The minimum intron length that may be found during closure search. The default is 50.\n+ --max-closure-intron The maximum intron length that may be found during closure search. The default is 5000.\n+ --min-coverage-intron The minimum intron length that may be found during coverage search. The default is 50.\n+ --max-coverage-intron The maximum intron length that may be found during coverage search. The default is 20000.\n+ --min-segment-intron The minimum intron length that may be found during split-segment search. The default is 50.\n+ --max-segment-intron The maximum intron length that may be found during split-segment search. The default is 500000.\n+ </help>\n+</tool>\n' |