| Previous changeset 14:2fe07f50a41e (2014-12-01) Next changeset 16:b5f1f599d1fb (2015-07-22) |
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Commit message:
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) |
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modified:
test-data/blastn_rhodopsin_vs_three_human.xml test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastx_rhodopsin_vs_four_human.xml test-data/blastx_rhodopsin_vs_four_human_all.tabular test-data/four_human_proteins.fasta test-data/tblastn_four_human_vs_rhodopsin.html test-data/tblastn_four_human_vs_rhodopsin.xml tool-data/blastdb.loc.sample tool-data/blastdb_d.loc.sample tool-data/blastdb_p.loc.sample tools/ncbi_blast_plus/README.rst tools/ncbi_blast_plus/blastxml_to_tabular.py tools/ncbi_blast_plus/blastxml_to_tabular.xml tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml tools/ncbi_blast_plus/ncbi_macros.xml tools/ncbi_blast_plus/ncbi_makeblastdb.xml tools/ncbi_blast_plus/ncbi_makeprofiledb.xml tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml tools/ncbi_blast_plus/repository_dependencies.xml tools/ncbi_blast_plus/tool_dependencies.xml |
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added:
test-data/blastdb.loc test-data/blastdb_d.loc test-data/blastdb_p.loc test-data/blastn_chimera_vs_three_human_max1.tabular test-data/blastn_chimera_vs_three_human_max1.txt test-data/chimera.fasta test-data/four_human_proteins.dbinfo.txt test-data/three_human_mRNA.dbinfo.txt test-data/three_human_mRNA.fasta.log.txt test-data/three_human_mRNA.fasta.nhd test-data/three_human_mRNA.fasta.nhi test-data/three_human_mRNA.fasta.nhr test-data/three_human_mRNA.fasta.nin test-data/three_human_mRNA.fasta.nog test-data/three_human_mRNA.fasta.nsd test-data/three_human_mRNA.fasta.nsi test-data/three_human_mRNA.fasta.nsq test-data/tool_data_table_conf.xml.test tool-data/tool_data_table_conf.xml.sample |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b test-data/blastdb.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastdb.loc Sun Jul 05 10:37:27 2015 -0400 |
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| @@ -0,0 +1,7 @@ +# This is a test file distributed with the Galaxy BLAST+ wrapper for +# defining a list of nucleotide BLAST databases used in functional +# tests for blastn etc. +# +# See the file tool-data/blastdb.loc.sample for more information. +# +three_human_mRNA Three Human mRNAs ${__HERE__}/three_human_mRNA.fasta |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b test-data/blastdb_d.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastdb_d.loc Sun Jul 05 10:37:27 2015 -0400 |
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| @@ -0,0 +1,7 @@ +# This is a test file distributed with the Galaxy BLAST+ wrapper for +# defining a list of protein domain BLAST databases used in functional +# tests of rpsblast etc. +# +# See the file tool-data/blastdb_d.loc.sample for more information. +# +cd00003_and_cd00008 Domains CD00003 (PNPsynthase) and CD00008 (PIN_53EXO-like) ${__HERE__}/cd00003_and_cd00008 |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b test-data/blastdb_p.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastdb_p.loc Sun Jul 05 10:37:27 2015 -0400 |
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| @@ -0,0 +1,8 @@ +# This is a test file distributed with the Galaxy BLAST+ wrapper for +# defining a list of protein BLAST databases used in functional tests +# for blastp etc. +# +# See the file tool-data/blastdb_p.loc.sample for more information. +# +four_human_proteins Four Human Proteins (no taxid) ${__HERE__}/four_human_proteins.fasta +four_human_proteins_taxid Four Human Proteins (with taxid) ${__HERE__}/four_human_proteins_taxid.fasta |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b test-data/blastn_chimera_vs_three_human_max1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastn_chimera_vs_three_human_max1.tabular Sun Jul 05 10:37:27 2015 -0400 |
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| @@ -0,0 +1,1 @@ +chimera ENA|AB011145|AB011145.1 100.00 4560 0 0 1 4560 121 4680 0.0 8421 |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b test-data/blastn_chimera_vs_three_human_max1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastn_chimera_vs_three_human_max1.txt Sun Jul 05 10:37:27 2015 -0400 |
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| b'@@ -0,0 +1,356 @@\n+BLASTN 2.2.30+\n+\n+\n+Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb\n+Miller (2000), "A greedy algorithm for aligning DNA sequences", J\n+Comput Biol 2000; 7(1-2):203-14.\n+\n+\n+\n+Database: Just 3 human mRNA sequences\n+ 3 sequences; 10,732 total letters\n+\n+\n+\n+Query= chimera chunks of AB011145 plus M10051 plus BC112106\n+\n+Length=9973\n+ Score E\n+Sequences producing significant alignments: (Bits) Value\n+\n+ ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein,... 8421 0.0 \n+\n+\n+> ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, \n+partial cds.\n+Length=4796\n+\n+ Score = 8421 bits (4560), Expect = 0.0\n+ Identities = 4560/4560 (100%), Gaps = 0/4560 (0%)\n+ Strand=Plus/Plus\n+\n+Query 1 GGACCCCAGCGTTACCATGCATCCTGCCGTCTTCCTATCCTTACCCGACCTCAGATGCTC 60\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 121 GGACCCCAGCGTTACCATGCATCCTGCCGTCTTCCTATCCTTACCCGACCTCAGATGCTC 180\n+\n+Query 61 CCTTCTGCTCCTGGTAACTTGGGTTTTTACTCCTGTAACAACTGAAATAACAAGTCTTGA 120\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 181 CCTTCTGCTCCTGGTAACTTGGGTTTTTACTCCTGTAACAACTGAAATAACAAGTCTTGA 240\n+\n+Query 121 TACAGAGAATATAGATGAAATTTTAAACAATGCTGATGTTGCTTTAGTAAATTTTTATGC 180\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 241 TACAGAGAATATAGATGAAATTTTAAACAATGCTGATGTTGCTTTAGTAAATTTTTATGC 300\n+\n+Query 181 TGACTGGTGTCGTTTCAGTCAGATGTTGCATCCAATTTTTGAGGAAGCTTCCGATGTCAT 240\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 301 TGACTGGTGTCGTTTCAGTCAGATGTTGCATCCAATTTTTGAGGAAGCTTCCGATGTCAT 360\n+\n+Query 241 TAAGGAAGAATTTCCAAATGAAAATCAAGTAGTGTTTGCCAGAGTTGATTGTGATCAGCA 300\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 361 TAAGGAAGAATTTCCAAATGAAAATCAAGTAGTGTTTGCCAGAGTTGATTGTGATCAGCA 420\n+\n+Query 301 CTCTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAATTGTTTCGTAA 360\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 421 CTCTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAATTGTTTCGTAA 480\n+\n+Query 361 TGGGATGATGATGAAGAGAGAATACAGGGGTCAGCGATCAGTGAAAGCATTGGCAGATTA 420\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 481 TGGGATGATGATGAAGAGAGAATACAGGGGTCAGCGATCAGTGAAAGCATTGGCAGATTA 540\n+\n+Query 421 CATCAGGCAACAAAAAAGTGACCCCATTCAAGAAATTCGGGACTTAGCAGAAATCACCAC 480\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 541 CATCAGGCAACAAAAAAGTGACCCCATTCAAGAAATTCGGGACTTAGCAGAAATCACCAC 600\n+\n+Query 481 TCTTGATCGCAGCAAAAGAAATATCATTGGATATTTTGAGCAAAAGGACTCGGACAACTA 540\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 601 TCTTGATCGCAGCAAAAGAAATATCATTGGATATTTTGAGCAAAAGGACTCGGACAACTA 660\n+\n+Query 541 TAGAGTTTTTGAACGAGTAGCGAATATTTTGCATGATGACTGTGCCTTTCTTTCTGCATT 600\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 661 TAGAGTTTTTGAACGAGTAGCGAATATTTTGCATGATGACTGTGCCTTTCTTTCTGCATT 720\n+\n+Query 601 TGGGGATGTTTCAAAACCGGAAAGATATAGTGGCGACAACATAATCTACAAACCACCAGG 660\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 721 TGGGGATGTTTCAAAACCGGAAAGATATAGTGGCGACAACATAATCTACAAACCACCAGG 780\n+\n+Query 661 GCATTCTGCTCCGGATATGGTGTACTTGGGAGCTATGACAAATTTTGATGTGACTTACAA 720\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 781 GCATTCTGCTCCGGATATGGTGTACTTGGGAGCTATGACAAATTTTGATGTGACTTACAA 840\n+\n+Query 721 TTGGATTCAAGATAAATGTGTTCCTCTTGTCCGAGAAATAACATTTGAAAATGGAGAGGA 780\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 841 TTGGATTCAAGATAAATGTGTTCCTCTTGTCCGAGAAATAACATTTGAAAATGGAGAGGA 900\n+\n+Query 781 ATTGACAGAAGAAGGACTGCCTTTTCTCATACTCTTTCACATGAAAGAAGATACAGAA'..b'3780\n+\n+Query 3661 GACAAAATAAAGGTTAAAGAGGGCATAAAGGAGCACTCAATTGCAGAGATTTGAGGACAT 3720\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 3781 GACAAAATAAAGGTTAAAGAGGGCATAAAGGAGCACTCAATTGCAGAGATTTGAGGACAT 3840\n+\n+Query 3721 TATTTTTATTTTGAGCTTTAAAAAGATGAATAGGTGTTCTCAGGAGGTAGGGATCTGGCT 3780\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 3841 TATTTTTATTTTGAGCTTTAAAAAGATGAATAGGTGTTCTCAGGAGGTAGGGATCTGGCT 3900\n+\n+Query 3781 GAGAGGGAATAATCTGAGCAAAGGTATGAAACAGCCTAATGCATTAGAGAAAAAAGTTCT 3840\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 3901 GAGAGGGAATAATCTGAGCAAAGGTATGAAACAGCCTAATGCATTAGAGAAAAAAGTTCT 3960\n+\n+Query 3841 TTTAGTAAGGCATTTGGGGTTGGGGAAGCTAGAAAAAGAAATGGGAGCTGGTCACACAGG 3900\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 3961 TTTAGTAAGGCATTTGGGGTTGGGGAAGCTAGAAAAAGAAATGGGAGCTGGTCACACAGG 4020\n+\n+Query 3901 GCCTTGTGTGCCAGACTAAGGGGTTTGTAGTATATATTGTAGGCAGAAGAGATCCATCAA 3960\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 4021 GCCTTGTGTGCCAGACTAAGGGGTTTGTAGTATATATTGTAGGCAGAAGAGATCCATCAA 4080\n+\n+Query 3961 CAGATTGCAAGCAAGGAAGTATGTTCACTTTAAAGTTTGAGAAAGAATAGTGTGGAAGCA 4020\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 4081 CAGATTGCAAGCAAGGAAGTATGTTCACTTTAAAGTTTGAGAAAGAATAGTGTGGAAGCA 4140\n+\n+Query 4021 CGTCTCAAATTTAGACTTACTTGTTCCCCCTCTGAACCGTGAATCAGACCATTTCAGGTA 4080\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 4141 CGTCTCAAATTTAGACTTACTTGTTCCCCCTCTGAACCGTGAATCAGACCATTTCAGGTA 4200\n+\n+Query 4081 GAAGTCTTCCCCGGTTTATCTGATCTACTCGGGGCCTCAGGCTTCTCAGCTGGGAAGAGA 4140\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 4201 GAAGTCTTCCCCGGTTTATCTGATCTACTCGGGGCCTCAGGCTTCTCAGCTGGGAAGAGA 4260\n+\n+Query 4141 GGATGCAAGACCAGACTGAAGAACACGGTTGAGTCCCCAGAACCAAAAGGGGGCCTTTCT 4200\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 4261 GGATGCAAGACCAGACTGAAGAACACGGTTGAGTCCCCAGAACCAAAAGGGGGCCTTTCT 4320\n+\n+Query 4201 GCTTCTTAGCCAGCTACCTCTTCGAGTTTTTCAAATTGTGAGGGGGACCATAAAAGGATG 4260\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 4321 GCTTCTTAGCCAGCTACCTCTTCGAGTTTTTCAAATTGTGAGGGGGACCATAAAAGGATG 4380\n+\n+Query 4261 GAAACTTTTAGATGACATTCTACAAATTAtttttttCTTTAAATTAAAAGAACCTAGCCA 4320\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 4381 GAAACTTTTAGATGACATTCTACAAATTATTTTTTTCTTTAAATTAAAAGAACCTAGCCA 4440\n+\n+Query 4321 ATAAGATAGAGAATGGGCATCTAAGGCATCTCAGAGCTCTCTGATGAAGCCAGGTTGTCA 4380\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 4441 ATAAGATAGAGAATGGGCATCTAAGGCATCTCAGAGCTCTCTGATGAAGCCAGGTTGTCA 4500\n+\n+Query 4381 AAGATCATTTGCAAAAGAAGGGAAAACTGGCATGACAAAAGCTACAGAGAGGAGAGTGAA 4440\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 4501 AAGATCATTTGCAAAAGAAGGGAAAACTGGCATGACAAAAGCTACAGAGAGGAGAGTGAA 4560\n+\n+Query 4441 ATATAGAAGTGTTTGAAATGTTCAAGCTCACAATAAGCTTAAATTTATAGAAAATGCTAA 4500\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 4561 ATATAGAAGTGTTTGAAATGTTCAAGCTCACAATAAGCTTAAATTTATAGAAAATGCTAA 4620\n+\n+Query 4501 GGTTGTCAAGAAGGCttttttttttttcttttttAAACCTGAGGGCAAAAAGGAATGGAT 4560\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Sbjct 4621 GGTTGTCAAGAAGGCTTTTTTTTTTTTCTTTTTTAAACCTGAGGGCAAAAAGGAATGGAT 4680\n+\n+\n+\n+Lambda K H\n+ 1.33 0.621 1.12 \n+\n+Gapped\n+Lambda K H\n+ 1.28 0.460 0.850 \n+\n+Effective search space used: 106299490\n+\n+\n+ Database: Just 3 human mRNA sequences\n+ Posted date: Dec 26, 2014 5:54 AM\n+ Number of letters in database: 10,732\n+ Number of sequences in database: 3\n+\n+\n+\n+Matrix: blastn matrix 1 -2\n+Gap Penalties: Existence: 0, Extension: 2.5\n' |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b test-data/blastn_rhodopsin_vs_three_human.xml --- a/test-data/blastn_rhodopsin_vs_three_human.xml Mon Dec 01 05:59:16 2014 -0500 +++ b/test-data/blastn_rhodopsin_vs_three_human.xml Sun Jul 05 10:37:27 2015 -0400 |
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| @@ -2,7 +2,7 @@ <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>blastn</BlastOutput_program> - <BlastOutput_version>BLASTN 2.2.29+</BlastOutput_version> + <BlastOutput_version>BLASTN 2.2.30+</BlastOutput_version> <BlastOutput_reference>Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>Query_1</BlastOutput_query-ID> |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b test-data/blastp_four_human_vs_rhodopsin.xml --- a/test-data/blastp_four_human_vs_rhodopsin.xml Mon Dec 01 05:59:16 2014 -0500 +++ b/test-data/blastp_four_human_vs_rhodopsin.xml Sun Jul 05 10:37:27 2015 -0400 |
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| @@ -2,7 +2,7 @@ <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>blastp</BlastOutput_program> - <BlastOutput_version>BLASTP 2.2.29+</BlastOutput_version> + <BlastOutput_version>BLASTP 2.2.30+</BlastOutput_version> <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>sp|Q9BS26|ERP44_HUMAN</BlastOutput_query-ID> |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b test-data/blastx_rhodopsin_vs_four_human.xml --- a/test-data/blastx_rhodopsin_vs_four_human.xml Mon Dec 01 05:59:16 2014 -0500 +++ b/test-data/blastx_rhodopsin_vs_four_human.xml Sun Jul 05 10:37:27 2015 -0400 |
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| @@ -2,7 +2,7 @@ <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>blastx</BlastOutput_program> - <BlastOutput_version>BLASTX 2.2.29+</BlastOutput_version> + <BlastOutput_version>BLASTX 2.2.30+</BlastOutput_version> <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>Query_1</BlastOutput_query-ID> |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b test-data/blastx_rhodopsin_vs_four_human_all.tabular --- a/test-data/blastx_rhodopsin_vs_four_human_all.tabular Mon Dec 01 05:59:16 2014 -0500 +++ b/test-data/blastx_rhodopsin_vs_four_human_all.tabular Sun Jul 05 10:37:27 2015 -0400 |
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| b'@@ -1,10 +1,10 @@\n-gi|57163782|ref|NM_001009242.1|\tsp|P08100|OPSD_HUMAN\t96.55\t348\t12\t0\t1\t1044\t1\t348\t0.0\t 639\tsp|P08100|OPSD_HUMAN\t1647\t336\t343\t0\t98.56\t1\t0\tMNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\t1047\t348\tN/A\t0\tgi|57163782|ref|NM_001009242.1|\tgi|57163782|ref|NM_001009242.1|\t0\t0\tsp|P08100|OPSD_HUMAN\tsp|P08100|OPSD_HUMAN\tsp|P08100|OPSD_HUMAN\tN/A\tN/A\t1/0\t15KA71FL4TS79VA9ML34VI71LI7SASA21LI13TA1GV11\t99\t99\tN/A\tN/A\tN/A\tN/A\tN/A\n-gi|2734705|gb|U59921.1|BBU59921\tsp|P08100|OPSD_HUMAN\t85.24\t332\t49\t0\t42\t1037\t1\t332\t0.0\t 551\tsp|P08100|OPSD_HUMAN\t1419\t283\t315\t0\t94.88\t3\t0\tMNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE\t1574\t348\tN/A\t0\tgi|2734705|gb|U59921.1|BBU59921\tgi|2734705|gb|U59921.1|BBU59921\t0\t0\tsp|P08100|OPSD_HUMAN\tsp|P08100|OPSD_HUMAN\tsp|P08100|OPSD_HUMAN\tN/A\tN/A\t3/0\t10IV1MF2KA20YF1IM1CA7LV7ML5IV17FV1NDHL4CG3VS1ML1ST1MLNH3IVLF1AP3YNVL36SG4VI7IV3SA2VA3LA9ML5VI26LM8RQ2CF30VIFA13FY2STNH3EN7VI7SASA9LM8IL2LI6FL1ED1DE\t63\t63\tN/A\tN/A\tN/A\tN/A\tN/A\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t96.40\t111\t4\t0\t1\t333\t11\t121\t3e-67\t 220\tsp|P08100|OPSD_HUMAN\t561\t107\t109\t0\t98.20\t1\t0\tVPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG\t4301\t348\tN/A\t0\tgi|283855845|gb|GQ290303.1|\tgi|283855845|gb|GQ290303.1|\t0\t0\tsp|P08100|OPSD_HUMAN\tsp|P08100|OPSD_HUMAN\tsp|P08100|OPSD_HUMAN\tN/A\tN/A\t1/0\t5KA9HY61FL4TS28\t22\t8\tN/A\tN/A\tN/A\tN/A\tN/A\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t92.31\t65\t5\t0\t3174\t3368\t248\t312\t2e-35\t 127\tsp|P08100|OPSD_HUMAN\t319\t60\t64\t0\t98.46\t3\t0\tKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ\tKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ\t4301\t348\tN/A\t0\tgi|283855845|gb|GQ290303.1|\tgi|283855845|gb|GQ290303.1|\t0\t0\tsp|P08100|OPSD_HUMAN\tsp|P08100|OPSD_HUMAN\tsp|P08100|OPSD_HUMAN\tN/A\tN/A\t3/0\t18LV3GS19LI7SASA13\t22\t5\tN/A\tN/A\tN/A\tN/A\tN/A\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t91.53\t59\t5\t0\t2855\t3031\t177\t235\t2e-33\t 121\tsp|P08100|OPSD_HUMAN\t304\t54\t57\t0\t96.61\t2\t0\tRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS\tRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA\t4301\t348\tN/A\t0\tgi|283855845|gb|GQ290303.1|\tgi|283855845|gb|GQ290303.1|\t0\t0\tsp|P08100|OPSD_HUMAN\tsp|P08100|OPSD_HUMAN\tsp|P08100|OPSD_HUMAN\tN/A\tN/A\t2/0\t6ML34VI14VARASA\t22\t4\tN/A\tN/A\tN/A\tN/A\tN/A\n-gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t93.22\t59\t4\t0\t1404\t1580\t119\t177\t1e-25\t97.1\tsp|P08100|OPSD_HUMAN\t240\t55\t56\t0\t94.92\t3\t0\tLAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR\tLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR\t4301\t348\tN/A\t0\tgi|283855845|gb|GQ290303.1|\tgi|283855845|gb|GQ29030'..b'7.1\tsp|P08100|OPSD_HUMAN\t240\t55\t56\t0\t94.92\t3\t0\tLAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR\tLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR\t4301\t348\tN/A\t0\tgi|283855845|gb|GQ290303.1|\tgi|283855845|gb|GQ290303.1|\t0\t0\tsp|P08100|OPSD_HUMAN\tsp|P08100|OPSD_HUMAN\tsp|P08100|OPSD_HUMAN\tN/A\tN/A\t3/0\t1AG36LV1LF13VA4\t22\t1\tN/A\tN/A\tN/A\tN/A\tN/A\n+gi|283855845|gb|GQ290303.1|\tsp|P08100|OPSD_HUMAN\t88.46\t26\t3\t0\t4222\t4299\t312\t337\t1e-12\t57.0\tsp|P08100|OPSD_HUMAN\t136\t23\t24\t0\t92.31\t1\t0\tQFRNCMLTTLCCGKNPLGDDEASTTA\tQFRNCMLTTICCGKNPLGDDEASATV\t4301\t348\tN/A\t0\tgi|283855845|gb|GQ290303.1|\tgi|283855845|gb|GQ290303.1|\t0\t0\tsp|P08100|OPSD_HUMAN\tsp|P08100|OPSD_HUMAN\tsp|P08100|OPSD_HUMAN\tN/A\tN/A\t1/0\t9LI13TA1AV\t22\t1\tN/A\tN/A\tN/A\tN/A\tN/A\n+gi|283855822|gb|GQ290312.1|\tsp|P08100|OPSD_HUMAN\t95.09\t326\t16\t0\t1\t978\t11\t336\t0.0\t 589\tsp|P08100|OPSD_HUMAN\t1518\t310\t322\t0\t98.77\t1\t0\tVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT\t983\t348\tN/A\t0\tgi|283855822|gb|GQ290312.1|\tgi|283855822|gb|GQ290312.1|\t0\t0\tsp|P08100|OPSD_HUMAN\tsp|P08100|OPSD_HUMAN\tsp|P08100|OPSD_HUMAN\tN/A\tN/A\t1/0\t5KA66ND4FL4TS5ML7AP49LV25ML34VI40VI6LV19VI11SASA21LI13TA1\t99\t33\tN/A\tN/A\tN/A\tN/A\tN/A\n+gi|18148870|dbj|AB062417.1|\tsp|P08100|OPSD_HUMAN\t93.39\t348\t23\t0\t1\t1044\t1\t348\t0.0\t 619\tsp|P08100|OPSD_HUMAN\t1596\t325\t337\t0\t96.84\t1\t0\tMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\t1047\t348\tN/A\t0\tgi|18148870|dbj|AB062417.1|\tgi|18148870|dbj|AB062417.1|\t0\t0\tsp|P08100|OPSD_HUMAN\tsp|P08100|OPSD_HUMAN\tsp|P08100|OPSD_HUMAN\tN/A\tN/A\t1/0\t15KA9AY22MV38FL4TS79VA9ML10PLHKEP1TV14IT2LM1VI47LV3GS11DN14TSSA1VI17VL2LI13TA13\t99\t33\tN/A\tN/A\tN/A\tN/A\tN/A\n+gi|12583664|dbj|AB043817.1|\tsp|P08100|OPSD_HUMAN\t81.68\t333\t61\t0\t23\t1021\t1\t333\t0.0\t 532\tsp|P08100|OPSD_HUMAN\t1371\t272\t307\t0\t92.19\t2\t0\tMNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDG\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA\t1344\t348\tN/A\t0\tgi|12583664|dbj|AB043817.1|\tgi|12583664|dbj|AB043817.1|\t0\t0\tsp|P08100|OPSD_HUMAN\tsp|P08100|OPSD_HUMAN\tsp|P08100|OPSD_HUMAN\tN/A\tN/A\t2/0\t10IV1MF22AQ2AM1SA4FL2IVAL12IVEQ23FL4TS1ML3ML12IL14CS8WYMV5VMTS6SN6MAVF2TV6LA3FA20RLAK1GEIV10TVCV2ST2LMAIVI1SF4RQ2CF12EA3RK2RK6VI4SA2VI9WF8TN9SA5SA1LI3MV3CM6HN2IL2LI6FLEGEDEDDEGA\t74\t25\tN/A\tN/A\tN/A\tN/A\tN/A\n' |
| b |
| diff -r 2fe07f50a41e -r c16c30e9ad5b test-data/chimera.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chimera.fasta Sun Jul 05 10:37:27 2015 -0400 |
| b |
| b'@@ -0,0 +1,168 @@\n+>chimera chunks of AB011145 plus M10051 plus BC112106\n+GGACCCCAGCGTTACCATGCATCCTGCCGTCTTCCTATCCTTACCCGACCTCAGATGCTC\n+CCTTCTGCTCCTGGTAACTTGGGTTTTTACTCCTGTAACAACTGAAATAACAAGTCTTGA\n+TACAGAGAATATAGATGAAATTTTAAACAATGCTGATGTTGCTTTAGTAAATTTTTATGC\n+TGACTGGTGTCGTTTCAGTCAGATGTTGCATCCAATTTTTGAGGAAGCTTCCGATGTCAT\n+TAAGGAAGAATTTCCAAATGAAAATCAAGTAGTGTTTGCCAGAGTTGATTGTGATCAGCA\n+CTCTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAATTGTTTCGTAA\n+TGGGATGATGATGAAGAGAGAATACAGGGGTCAGCGATCAGTGAAAGCATTGGCAGATTA\n+CATCAGGCAACAAAAAAGTGACCCCATTCAAGAAATTCGGGACTTAGCAGAAATCACCAC\n+TCTTGATCGCAGCAAAAGAAATATCATTGGATATTTTGAGCAAAAGGACTCGGACAACTA\n+TAGAGTTTTTGAACGAGTAGCGAATATTTTGCATGATGACTGTGCCTTTCTTTCTGCATT\n+TGGGGATGTTTCAAAACCGGAAAGATATAGTGGCGACAACATAATCTACAAACCACCAGG\n+GCATTCTGCTCCGGATATGGTGTACTTGGGAGCTATGACAAATTTTGATGTGACTTACAA\n+TTGGATTCAAGATAAATGTGTTCCTCTTGTCCGAGAAATAACATTTGAAAATGGAGAGGA\n+ATTGACAGAAGAAGGACTGCCTTTTCTCATACTCTTTCACATGAAAGAAGATACAGAAAG\n+TTTAGAAATATTCCAGAATGAAGTAGCTCGGCAATTAATAAGTGAAAAAGGTACAATAAA\n+CTTTTTACATGCCGATTGTGACAAATTTAGACATCCTCTTCTGCACATACAGAAAACTCC\n+AGCAGATTGTCCTGTAATCGCTATTGACAGCTTTAGGCATATGTATGTGTTTGGAGACTT\n+CAAAGATGTATTAATTCCTGGAAAACTCAAGCAATTCGTATTTGACTTACATTCTGGAAA\n+ACTGCACAGAGAATTCCATCATGGACCTGACCCAACTGATACAGCCCCAGGAGAGCAAGC\n+CCAAGATGTAGCAAGCAGTCCACCTGAGAGCTCCTTCCAGAAACTAGCACCCAGTGAATA\n+TAGGTATACTCTATTGAGGGATCGAGATGAGCTTTAAAAACTTGAAAAACAGTTTGTAAG\n+CCTTTCAACAGCAGCATCAACCTACGTGGTGGAAATAGTAAACCTATATTTTCATAATTC\n+TATGTGTATTTTTATTTTGAATAAACAGAAAGAAATTTTGGGTTTTTAATTTTTTTCTCC\n+CCGACTCAAAATGCATTGTCATTTAATATAGTAGCCTCTTAAAAAAAAAAAAACCTGCTA\n+GGATTTAAAAATAAAAATCAGAGGCCTATCTCCACTTTAAATCTGTCCTGTAAAAGTTTT\n+ATAAATCAAATGAAAGGTGACATTGCCAGAAACTTACCATTAACTTGCACTACTAGGGTA\n+GGGAGGACTTAGGATGTTTCCTGTGTCGTATGTGCTTTTCTTTCTTTCATATGATCAATT\n+CTGTTGGTATTTTCAGTATCTCATTTCTCAAAGCTAAAGAGATATACATTCTGGATACTT\n+GGGAGGGGAATAAATTAAAGTTTTCACACTGTGTACTGTGTTTTACTGATTGGTTGGATA\n+TTGCTTATGAAAATTCCATAGTGGTATTTTTTTGGATTCTTAATGTGTAACTTAAACATA\n+CTTTGAAGTGGAGGAGAGTCATAAGACAGAACATTTGGCAGGAATTGTCCTTATGAAACA\n+AGAAAAAGAAAATGAAAAGTATTATTAAGCTTCTGTGTTTGTCTAAAAATGTGGCATATG\n+GATGGCATTTAAAACTTTGAATGAATTATACCTAAATCTGGGACAGGGAGGTGACAGTGG\n+AACAGGCTACCAATCAGAACTAGATGACTTTTAAGGCTCCTCCTATTATGAGACTTCAAT\n+TTCCAAAGAGAAGAACTAGCAGAGAAATTGTATTTCAGTAATTTTAAGCTCCTTCTGTCT\n+TGTAGAGTCTTGTTATAGTTGTATAAATCAAAAACACAGAATAAGGAACATATTTAACTT\n+TTTTTCATTATAAAATGGTTAGAGGACCCTACCCCCTCTAGATTCCCTGATTTCCCCAGG\n+CCTGCAGCATACAGTAAGATGGGTCCCTGTGCCAGGCCTCAATACTGCCAGGGAATAAAA\n+CCAGAGGGAGAGGACCCTCAGTGTCATATCAGGAAGCCCAGTGCCAGAGGACAGACAGGT\n+TCAAAACTGGCTTTTCCTCTGGGCCTGGGTTGGTGCTATAGGCCAAGGGTCATTTTATAC\n+TTGGGTATAAATCAATCCCAGTTTGGGAAAAGATTATTTTTAAGCTTAAAAGGCTGACAT\n+GTGCCATTATATGTAGTATGTAATATATGTAACATCTTCCAATTCTTTTAAAATAAAATT\n+AATATTTATAATGGATATTTAATGATTGTTATTTTTAAAAACCAGCTTATAATTCCTCGT\n+TATGCATGATTTATCCAAAGTTTCCATAGTTTTATTCAAAATAATAAATGTTAATAAGGT\n+GATAAGGGGTATATTTAATGTATTGTATCAAATTGTGAATAAGAAAGTAGGATGGAGCTT\n+TCTAGAGGTTGGGCCTTAGTTCTGTTATCCTCATTGCTTTTAACCAATAAGTTAAATGAA\n+GTTAGAGTTATGGTCTTCAGGTTAGATTATGGACCAGATCTGTGAGGGTCAGCATGGAAA\n+TTCACATTCAACAAGGTAGCACACAGGACCAAGAGCAGCACATGCAATCAACTGGAATAA\n+TATAGTAATCCTGTAACTGGGTTTGAAAAAATAATCAACAAAAGATACAATTCAAGGGTT\n+AGGTTGCAGAGAGCTGGCTTGAGAGTAGTTATTATGAAAAAGGCCTCAAGGAGTACGTGT\n+TCAGTATGCTCTAAGATGATAAAGTGGCTGTTAAAAAGGGAGTTGATTTGAGGAAGTATT\n+ACTTAGCATTCATGCATATTGGGCTTAGGCTCTAGCCCTGCCACTATCATTGTCTTCTCT\n+GGACTGTGAAGTCACTGAGGACAAGGAAACTAAATTTAATGTCTGTATCACTAGTGCCTA\n+GAATTTCTGGACACTTAGTAGTCACCATCAGGCGTTTATTTAATGAATGAGAAGCAAAGT\n+GACCTTGGTTACTTTTTTACCCTGAGGGGCTCAGCACTCATTAGGACTTGGTGCCTAATT\n+TTATAAAAAGTCACTAAGCTCAAGTGCTTGGATGAAAGGACAGCGTGGATAAAAAGGTTT\n+TTAAAACATGGATGTTAAGGCTGTTTTGCTTGGAGAAGACTTGGGACTGGGACAGTCTTT\n+AGATATTATTTGAAATGCTGGCACTGTCTATCTGGATCCCAGGGCTTGAACTAGGATTTG\n+AGGAAGTCACAGGGAAGCAGATTTCAGTCTGACATTTATTCAGTGCAAGTTTTTTGGTGC\n+TGTAGTATATGATGAAAGATGTAAAGCTGAATAAAGCATTATTTCTGCCCTAGAGTTGTT\n+CACAGCCTAGTCAGGCATATGGATATGTAAACAATGACTGTAACGTGTTATAGATGTAAA\n+GACAAAATAAAGGTTAAAGAGGGCATAAAGGAGCACTCAATTGCAGAGATTTGAGGACAT\n+TATTTTTATTTTGAGCTTTAAAAAGATGAATAGGTGTTCTCAGGAGGTAGGGATCTGGCT\n+GAGAGGGAATAATCTGAGC'..b'GGGGACAAGGCATCC\n+TGTGAAAATGAGTTACTTAAATTTTCTTACATTCGGACATCTTTTGACAAGATCTTGCTG\n+AGATGGGAGCCGTACTGGCCCCCCGACTTCCGAGACCTCTTGGGGTTCATGCTGTTCTAC\n+AAAGAGGCCCCTTATCAGAATGTGACGGAGTTCGATGGGCAGGATGCGTGTGGTTCCAAC\n+AGTTGGACGGTGGTAGACATTGACCCACCCCTGAGGTCCAACGACCCCAAATCACAGAAC\n+CACCCAGGGTGGCTGATGCGGGGTCTCAAGCCCTGGACCCAGTATGCCATCTTTGTGAAG\n+ACCCTGGTCACCTTTTCGGATGAACGCCGGACCTATGGGGCCAAGAGTGACATCATTTAT\n+GTCCAGACAGATGCCACCAACCCCTCTGTGCCCCTGGATCCAATCTCAGTGTCTAACTCA\n+TCATCCCAGATTATTCTGAAGTGGAAACCACCCTCCGACCCCAATGGCAACATCACCCAC\n+TACCTGGTTTTCTGGGAGAGGCAGGCGGAAGACAGTGAGCTGTTCGAGCTGGATTATTGC\n+CTCAAAGGGCTGAAGCTGCCCTCGAGGACCTGGTCTCCACCATTCGAGTCTGAAGATTCT\n+CAGAAGCACAACCAGAGTGAGTATGAGGATTCGGCCGGCGAATGCTGCTCCTGTCCAAAG\n+ACAGACTCTCAGATCCTGAAGGAGCTGGAGGAGTCCTCGTTTAGGAAGACGTTTGAGGAT\n+TACCTGCACAACGTGGTTTTCGTCCCCAGAAAAACCTCTTCAGGCACTGGTGCCGAGGAC\n+CCTAGGCCATCTCGGAAACGCAGGTCCCTTGGCGATGTTGGGAATGTGACGGTGGCCGTG\n+CCCACGGTGGCAGCTTTCCCCAACACTTCCTCGACCAGCGTGCCCACGAGTCCGGAGGAG\n+CACAGGCCTTTTGAGAAGGTGGTGAACAAGGAGTCGCTGGTCATCTCCGGCTTGCGACAC\n+TTCACGGGCTATCGCATCGAGCTGCAGGCTTGCAACCAGGACACCCCTGAGGAACGGTGC\n+AGTGTGGCAGCCTACGTCAGTGCGAGGACCATGCCTGAAGCCAAGGCTGATGACATTGTT\n+GGCCCTGTGACGCATGAAATCTTTGAGAACAACGTCGTCCACTTGATGTGGCAGGAGCCG\n+AAGGAGCCCAATGGTCTGATCGTGCTGTATGAAGTGAGTTATCGGCGATATGGTGATGAG\n+GAGCTGCATCTCTGCGTCTCCCGCAAGCACTTCGCTCTGGAACGGGGCTGCAGGCTGCGT\n+GGGCTGTCACCGGGGAACTACAGCGTGCGAATCCGGGCCACCTCCCTTGCGGGCAACGGC\n+TCTTGGACGGAACCCACCTATTTCTACGTGACAGACTATTTAGACGTCCCGTCAAATATT\n+GCAAAAATTATCATCGGCCCCCTCATCTTTGTCTTTCTCTTCAGTGTTGTGATTGGAAGT\n+ATTTATCTATTCCTGAGAAAGAGGCAGCCAGATGGGCCGCTGGGACCGCTTTACGCTTCT\n+TCAAACCCTGAGTATCTCAGTGCCAGTGATGTGTTTCCATGCTCTGTGTACGTGCCGGAC\n+GAGTGGGAGGTGTCTCGAGAGAAGATCACCCTCCTTCGAGAGCTGGGGCAGGGCTCCTTC\n+GGCATGGTGTATGAGGGCAATGCCAGGGACATCATCAAGGGTGAGGCAGAGACCCGCGTG\n+GCGGTGAAGACGGTCAACGAGTCAGCCAGTCTCCGAGAGCGGATTGAGTTCCTCAATGAG\n+GCCTCGGTCATGAAGGGCTTCACCTGCCATCACGTGGTGCGCCTCCTGGGAGTGGTGTCC\n+AAGGGCCAGCCCACGCTGGTGGTGATGGAGCTGATGGCTCACGGAGACCTGAAGAGCTAC\n+CTCCGTTCTCTGCGGCCAGAGGCTGAGAATAATCCTGGCCGCCCTCCCCCTACCCTTCAA\n+GAGATGATTCAGATGGCGGCAGAGATTGCTGACGGGATGGCCTACCTGAACGCCAAGAAG\n+TTTGTGCATCGGGACCTGGCAGCGAGAAACTGCATGGTCGCCCATGATTTTACTGTCAAA\n+ATTGGAGACTTTGGAATGACCAGAGACATCTATGAAACGGATTACTACCGGAAAGGGGGC\n+AAGGGTCTGCTCCCTGTACGGTGGATGGCACCGGAGTCCCTGAAGGATGGGGTCTTCACC\n+ACTTCTTCTGACATGTGGTCCTTTGGCGTGGTCCTTTGGGAAATCACCAGCTTGGCAGAA\n+CAGCCTTACCAAGGCCTGTCTAATGAACAGGTGTTGAAATTTGTCATGGATGGAGGGTAT\n+CTGGATCAACCCGACAACTGTCCAGAGAGAGTCACTGACCTCATGCGCATGTGCTGGCAA\n+TTCAACCCCAAGATGAGGCCAACCTTCCTGGAGATTGTCAACCTGCTCAAGGACGACCTG\n+CACCCCAGCTTTCCAGAGGTGTCGTTCTTCCACAGCGAGGAGAACAAGGCTCCCGAGAGT\n+GAGGAGCTGGAGATGGAGTTTGAGGACATGGAGAATGTGCCCCTGGACCGTTCCTCGCAC\n+TGTCAGAGGGAGGAGGCGGGGGGCCGGGATGGAGGGTCCTCGCTGGGTTTCAAGCGGAGC\n+TACGAGGAACACATCCCTTACACACACATGAACGGAGGCAAGAAAAACGGGCGGATTCTG\n+ACCTTGCCTCGGTCCAATCCTTCCTAACAGTGCCTACCGTGGCGGGGGCGGGCAGGGGTT\n+CCCATTTTCGCTTTCCTCTGGTTTGAAAGCCTCTGGAAAACTCAGGATTCTCACGACTCT\n+CCCTTCTCCAATGCGACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTG\n+GCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTGGGC\n+TTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCT\n+CTCAACTACATCCTGCTCAACCTAGCCGTGGCTGACCTCTTCATGGTCCTAGGTGGCTTC\n+ACCAGCACCCTCTACACCTCTCTGCATGGATACTTCGTCTTCGGGCCCACAGGATGCAAT\n+TTGGAGGGCTTCTTTGCCACCCTGGGCGGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTG\n+GCCATCGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTCGGGGAGAAC\n+CATGCCATCATGGGCGTTGCCTTCACCTGGGTCATGGCGCTGGCCTGCGCCGCACCCCCA\n+CTCGCCGGCTGGTCCAGGTACATCCCCGAGGGCCTGCAGTGCTCGTGTGGAATCGACTAC\n+TACACGCTCAAGCCGGAGGTCAACAACGAGTCTTTTGTCATCTACATGTTCGTGGTCCAC\n+TTCACCATCCCCATGATTATCATCTTTTTCTGCTATGGGCAGCTCGTCTTCACCGTCAAG\n+GAGGCCGCTGCCCAGCAGCAGGAGTCAGCCACCACACAGAAGGCAGAGAAGGAGGTCACC\n+CGCATGGTCATCATCATGGTCATCGCTTTCCTGATCTGCTGGGTGCCCTACGCCAGCGTG\n+GCATTCTACATCTTCACCCACCAGGGCTCCAACTTCGGTCCCATCTTCATGACCATCCCA\n+GCGTTCTTTGCCAAGAGCGCCGCCATCTACAACCCTGTCATCTATATCATGATGAACAAG\n+CAGTTCCGGAACTGCATGCTCACCACCATCTGCTGCGGCAAGAACCCACTGGGTGACGAT\n+GAGGCCTCTGCTACCGTGTCCAAGACGGAGACGAGCCAGGTGGCCCCGGCCTAAGACCTG\n+CCTAGGACTCTGTGGCCGACTATAGGCGTCTCCCATCCCCTACACCTTCCCCCAGCCACA\n+GCCATCCCACCAG\n' |
| b |
| diff -r 2fe07f50a41e -r c16c30e9ad5b test-data/four_human_proteins.dbinfo.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/four_human_proteins.dbinfo.txt Sun Jul 05 10:37:27 2015 -0400 |
| b |
| @@ -0,0 +1,7 @@ +Database: Just 4 human proteins + 4 sequences; 3,297 total residues + +Date: Feb 10, 2014 6:40 PM Longest sequence: 1,382 residues + +Volumes: + /mnt/galaxy/galaxy_blast/test-data/four_human_proteins_taxid.fasta |
| b |
| diff -r 2fe07f50a41e -r c16c30e9ad5b test-data/four_human_proteins.fasta --- a/test-data/four_human_proteins.fasta Mon Dec 01 05:59:16 2014 -0500 +++ b/test-data/four_human_proteins.fasta Sun Jul 05 10:37:27 2015 -0400 |
| b |
| @@ -1,61 +1,48 @@ >sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 -MHPAVFLSLPDLRCSLLLLVTWVFTPVTTEITSLDTENIDEILNNADVALVNFYADWCRF -SQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMK -REYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFER -VANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDK -CVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHAD -CDKFRHPLLHIQKTPADCPVIAIDSFRHMYVFGDFKDVLIPGKLKQFVFDLHSGKLHREF -HHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL +MHPAVFLSLPDLRCSLLLLVTWVFTPVTTEITSLDTENIDEILNNADVALVNFYADWCRFSQMLHPIFEEASDVIKEEFP +NENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMKREYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSK +RNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDK +CVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHADCDKFRHPLLHIQKTPADCPV +IAIDSFRHMYVFGDFKDVLIPGKLKQFVFDLHSGKLHREFHHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLL +RDRDEL >sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 -MKKFSRMPKSEGGSGGGAAGGGAGGAGAGAGCGSGGSSVGVRVFAVGRHQVTLEESLAEG -GFSTVFLVRTHGGIRCALKRMYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSIS -DNVWEVLILMEYCRAGQVVNQMNKKLQTGFTEPEVLQIFCDTCEAVARLHQCKTPIIHRD -LKVENILLNDGGNYVLCDFGSATNKFLNPQKDGVNVVEEEIKKYTTLSYRAPEMINLYGG -KPITTKADIWALGCLLYKLCFFTLPFGESQVAICDGNFTIPDNSRYSRNIHCLIRFMLEP -DPEHRPDIFQVSYFAFKFAKKDCPVSNINNSSIPSALPEPMTASEAAARKSQIKARITDT -IGPTETSIAPRQRPKANSATTATPSVLTIQSSATPVKVLAPGEFGNHRPKGALRPGNGPE -ILLGQGPPQQPPQQHRVLQQLQQGDWRLQQLHLQHRHPHQQQQQQQQQQQQQQQQQQQQQ -QQQQQQHHHHHHHHLLQDAYMQQYQHATQQQQMLQQQFLMHSVYQPQPSASQYPTMMPQY -QQAFFQQQMLAQHQPSQQQASPEYLTSPQEFSPALVSYTSSLPAQVGTIMDSSYSANRSV -ADKEAIANFTNQKNISNPPDMSGWNPFGEDNFSKLTEEELLDREFDLLRSNRLEERASSD -KNVDSLSAPHNHPPEDPFGSVPFISHSGSPEKKAEHSSINQENGTANPIKNGKTSPASKD -QRTGKKTSVQGQVQKGNDESESDFESDPPSPKSSEEEEQDDEEVLQGEQGDFNDDDTEPE -NLGHRPLLMDSEDEEEEEKHSSDSDYEQAKAKYSDMSSVYRDRSGSGPTQDLNTILLTSA -QLSSDVAVETPKQEFDVFGAVPFFAVRAQQPQQEKNEKNLPQHRFPAAGLEQEEFDVFTK -APFSKKVNVQECHAVGPEAHTIPGYPKSVDVFGSTPFQPFLTSTSKSESNEDLFGLVPFD -EITGSQQQKVKQRSLQKLSSRQRRTKQDMSKSNGKRHHGTPTSTKKTLKPTYRTPERARR -HKKVGRRDSQSSNEFLTISDSKENISVALTDGKDRGNVLQPEESLLDPFGAKPFHSPDLS -WHPPHQGLSDIRADHNTVLPGRPRQNSLHGSFHSADVLKMDDFGAVPFTELVVQSITPHQ -SQQSQPVELDPFGAAPFPSKQ +MKKFSRMPKSEGGSGGGAAGGGAGGAGAGAGCGSGGSSVGVRVFAVGRHQVTLEESLAEGGFSTVFLVRTHGGIRCALKR +MYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSISDNVWEVLILMEYCRAGQVVNQMNKKLQTGFTEPEVLQIFC +DTCEAVARLHQCKTPIIHRDLKVENILLNDGGNYVLCDFGSATNKFLNPQKDGVNVVEEEIKKYTTLSYRAPEMINLYGG +KPITTKADIWALGCLLYKLCFFTLPFGESQVAICDGNFTIPDNSRYSRNIHCLIRFMLEPDPEHRPDIFQVSYFAFKFAK +KDCPVSNINNSSIPSALPEPMTASEAAARKSQIKARITDTIGPTETSIAPRQRPKANSATTATPSVLTIQSSATPVKVLA +PGEFGNHRPKGALRPGNGPEILLGQGPPQQPPQQHRVLQQLQQGDWRLQQLHLQHRHPHQQQQQQQQQQQQQQQQQQQQQ +QQQQQQHHHHHHHHLLQDAYMQQYQHATQQQQMLQQQFLMHSVYQPQPSASQYPTMMPQYQQAFFQQQMLAQHQPSQQQA +SPEYLTSPQEFSPALVSYTSSLPAQVGTIMDSSYSANRSVADKEAIANFTNQKNISNPPDMSGWNPFGEDNFSKLTEEEL +LDREFDLLRSNRLEERASSDKNVDSLSAPHNHPPEDPFGSVPFISHSGSPEKKAEHSSINQENGTANPIKNGKTSPASKD +QRTGKKTSVQGQVQKGNDESESDFESDPPSPKSSEEEEQDDEEVLQGEQGDFNDDDTEPENLGHRPLLMDSEDEEEEEKH +SSDSDYEQAKAKYSDMSSVYRDRSGSGPTQDLNTILLTSAQLSSDVAVETPKQEFDVFGAVPFFAVRAQQPQQEKNEKNL +PQHRFPAAGLEQEEFDVFTKAPFSKKVNVQECHAVGPEAHTIPGYPKSVDVFGSTPFQPFLTSTSKSESNEDLFGLVPFD +EITGSQQQKVKQRSLQKLSSRQRRTKQDMSKSNGKRHHGTPTSTKKTLKPTYRTPERARRHKKVGRRDSQSSNEFLTISD +SKENISVALTDGKDRGNVLQPEESLLDPFGAKPFHSPDLSWHPPHQGLSDIRADHNTVLPGRPRQNSLHGSFHSADVLKM +DDFGAVPFTELVVQSITPHQSQQSQPVELDPFGAAPFPSKQ >sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 -MATGGRRGAAAAPLLVAVAALLLGAAGHLYPGEVCPGMDIRNNLTRLHELENCSVIEGHL -QILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYAL -VIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNE -ECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECL -GNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQG -CHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGC -TVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETL -EIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQE -RNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQ -NVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFS -DERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWE -RQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQIL -KELEESSFRKTFEDYLHNVVFVPRKTSSGTGAEDPRPSRKRRSLGDVGNVTVAVPTVAAF -PNTSSTSVPTSPEEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYV -SARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCV -SRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIAKIIIG -PLIFVFLFSVVIGSIYLFLRKRQPDGPLGPLYASSNPEYLSASDVFPCSVYVPDEWEVSR -EKITLLRELGQGSFGMVYEGNARDIIKGEAETRVAVKTVNESASLRERIEFLNEASVMKG -FTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLRSLRPEAENNPGRPPPTLQEMIQMA -AEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDIYETDYYRKGGKGLLPV -RWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDN -CPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDDLHPSFPEVSFFHSEENKAPESEELEME -FEDMENVPLDRSSHCQREEAGGRDGGSSLGFKRSYEEHIPYTHMNGGKKNGRILTLPRSN -PS +MATGGRRGAAAAPLLVAVAALLLGAAGHLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPK +LIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDW +SRILDSVEDNYIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECL +GNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYT +MNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRS +YALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQE +RNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDACGSNSWTVVD +IDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIIL +KWKPPSDPNGNITHYLVFWERQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQIL +KELEESSFRKTFEDYLHNVVFVPRKTSSGTGAEDPRPSRKRRSLGDVGNVTVAVPTVAAFPNTSSTSVPTSPEEHRPFEK +VVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYVSARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGL +IVLYEVSYRRYGDEELHLCVSRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIAKIIIG +PLIFVFLFSVVIGSIYLFLRKRQPDGPLGPLYASSNPEYLSASDVFPCSVYVPDEWEVSREKITLLRELGQGSFGMVYEG +NARDIIKGEAETRVAVKTVNESASLRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLRSLRP +EAENNPGRPPPTLQEMIQMAAEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDIYETDYYRKGGKGLLPV +RWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDNCPERVTDLMRMCWQFNPKMR +PTFLEIVNLLKDDLHPSFPEVSFFHSEENKAPESEELEMEFEDMENVPLDRSSHCQREEAGGRDGGSSLGFKRSYEEHIP +YTHMNGGKKNGRILTLPRSNPS >sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 -MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY -VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG -GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP -EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES -ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI -YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA +MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLA +VADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFT +WVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES +ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTT +ICCGKNPLGDDEASATVSKTETSQVAPA |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b test-data/tblastn_four_human_vs_rhodopsin.html --- a/test-data/tblastn_four_human_vs_rhodopsin.html Mon Dec 01 05:59:16 2014 -0500 +++ b/test-data/tblastn_four_human_vs_rhodopsin.html Sun Jul 05 10:37:27 2015 -0400 |
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| @@ -3,7 +3,7 @@ <BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099"> <PRE> -<b>TBLASTN 2.2.29+</b> +<b>TBLASTN 2.2.30+</b> <b>Query=</b> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b test-data/tblastn_four_human_vs_rhodopsin.xml --- a/test-data/tblastn_four_human_vs_rhodopsin.xml Mon Dec 01 05:59:16 2014 -0500 +++ b/test-data/tblastn_four_human_vs_rhodopsin.xml Sun Jul 05 10:37:27 2015 -0400 |
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| @@ -2,7 +2,7 @@ <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>tblastn</BlastOutput_program> - <BlastOutput_version>TBLASTN 2.2.29+</BlastOutput_version> + <BlastOutput_version>TBLASTN 2.2.30+</BlastOutput_version> <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>Query_1</BlastOutput_query-ID> |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b test-data/three_human_mRNA.dbinfo.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/three_human_mRNA.dbinfo.txt Sun Jul 05 10:37:27 2015 -0400 |
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| @@ -0,0 +1,7 @@ +Database: Just 3 human mRNA sequences + 3 sequences; 10,732 total bases + +Date: Dec 26, 2014 5:54 AM Longest sequence: 4,796 bases + +Volumes: + /mnt/galaxy/galaxy_blast/test-data/three_human_mRNA.fasta |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b test-data/three_human_mRNA.fasta.log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/three_human_mRNA.fasta.log.txt Sun Jul 05 10:37:27 2015 -0400 |
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| @@ -0,0 +1,5 @@ +New DB title: Just 3 human mRNA sequences +Sequence type: Nucleotide +Keep Linkouts: T +Keep MBits: T +Maximum file size: 1000000000B |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b test-data/three_human_mRNA.fasta.nhd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/three_human_mRNA.fasta.nhd Sun Jul 05 10:37:27 2015 -0400 |
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| @@ -0,0 +1,3 @@ +12956943350 +13082197871 +19180330422 |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b test-data/three_human_mRNA.fasta.nhi |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b test-data/three_human_mRNA.fasta.nhr |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b test-data/three_human_mRNA.fasta.nin |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b test-data/three_human_mRNA.fasta.nog |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b test-data/three_human_mRNA.fasta.nsd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/three_human_mRNA.fasta.nsd Sun Jul 05 10:37:27 2015 -0400 |
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| @@ -0,0 +1,3 @@ +gnl|bl_ord_id|00 +gnl|bl_ord_id|11 +gnl|bl_ord_id|22 |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b test-data/three_human_mRNA.fasta.nsi |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b test-data/three_human_mRNA.fasta.nsq |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b test-data/tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tool_data_table_conf.xml.test Sun Jul 05 10:37:27 2015 -0400 |
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| @@ -0,0 +1,15 @@ +<tables> + <!-- test files! --> + <table name="blastdb" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/blastdb.loc" /> + </table> + <table name="blastdb_p" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/blastdb_p.loc" /> + </table> + <table name="blastdb_d" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/blastdb_d.loc" /> + </table> +</tables> |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b tool-data/blastdb.loc.sample --- a/tool-data/blastdb.loc.sample Mon Dec 01 05:59:16 2014 -0500 +++ b/tool-data/blastdb.loc.sample Sun Jul 05 10:37:27 2015 -0400 |
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| @@ -1,39 +1,44 @@ -#This is a sample file distributed with Galaxy that is used to define a -#list of nucleotide BLAST databases, using three columns tab separated -#(longer whitespace are TAB characters): +# This is a sample file distributed with Galaxy that is used to define a +# list of nucleotide BLAST databases, using three columns tab separated: # -#<unique_id> <database_caption> <base_name_path> +# <unique_id>{tab}<database_caption>{tab}<base_name_path> +# +# The captions typically contain spaces and might end with the build date. +# It is important that the actual database name does not have a space in +# it, and that there are only two tabs on each line. # -#The captions typically contain spaces and might end with the build date. -#It is important that the actual database name does not have a space in -#it, and that there are only two tabs on each line. +# You can download the NCBI provided protein databases like NR from here: +# ftp://ftp.ncbi.nlm.nih.gov/blast/db/ # -#So, for example, if your database is nt and the path to your base name -#is /depot/data2/galaxy/blastdb/nt/nt.chunk, then the blastdb.loc entry -#would look like this: -# -#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk -# -#and your /depot/data2/galaxy/blastdb/nt directory would contain all of -#your "base names" (e.g.): +# For simplicity, many Galaxy servers are configured to offer just a live +# version of each NCBI BLAST database (updated with the NCBI provided +# Perl scripts or similar). In this case, we recommend using the case +# sensistive base-name of the NCBI BLAST databases as the unique id. +# Consistent naming is important for sharing workflows between Galaxy +# servers. # -#-rw-r--r-- 1 wychung galaxy 23437408 2008-04-09 11:26 nt.chunk.00.nhr -#-rw-r--r-- 1 wychung galaxy 3689920 2008-04-09 11:26 nt.chunk.00.nin -#-rw-r--r-- 1 wychung galaxy 251215198 2008-04-09 11:26 nt.chunk.00.nsq -#...etc... +# For example, consider the NCBI partially non-redundant nucleotide +# nt BLAST database, where you have downloaded and decompressed the +# files under /data/blastdb/ meaning at the command line BLAST+ would +# would look at the files /data/blastdb/nt.n* when run with: # -#Your blastdb.loc file should include an entry per line for each "base name" -#you have stored. For example: +# $ blastn -db /data/blastdb/nt -query ... +# +# In this case use nr (lower case to match the NCBI file naming) as the +# unique id in the first column of blastdb_p.loc, giving an entry like +# this: +# +# nt{tab}NCBI partially non-redundant (nt){tab}/data/blastdb/nt # -#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk -#wgs_30_Nov_2009 wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk -#test_20_Sep_2008 test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test -#...etc... +# Alternatively, rather than a "live" mirror of the NCBI databases which +# are updated automatically, for full reproducibility the Galaxy Team +# recommend saving date-stamped copies of the databases. In this case +# your blastdb.loc file should include an entry per line for each +# version you have stored. For example: # -#You can download the NCBI provided protein databases like NT from here: -#ftp://ftp.ncbi.nlm.nih.gov/blast/db/ +# nt_05Jun2010{tab}NCBI nt (partially non-redundant) 05 Jun 2010{tab}/data/blastdb/05Jun2010/nt +# nt_15Aug2010{tab}NCBI nt (partially non-redundant) 15 Aug 2010{tab}/data/blastdb/15Aug2010/nt +# ...etc... # -#See also blastdb_p.loc which is for any protein BLAST database, and -#blastdb_d.loc which is for any protein domains databases (like CDD). - - +# See also blastdb_p.loc which is for any protein BLAST database, and +# blastdb_d.loc which is for any protein domains databases (like CDD). |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b tool-data/blastdb_d.loc.sample --- a/tool-data/blastdb_d.loc.sample Mon Dec 01 05:59:16 2014 -0500 +++ b/tool-data/blastdb_d.loc.sample Sun Jul 05 10:37:27 2015 -0400 |
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| @@ -1,35 +1,57 @@ -#This is a sample file distributed with Galaxy that is used to define a -#list of protein domain databases, using three columns tab separated -#(longer whitespace are TAB characters): +# This is a sample file distributed with Galaxy that is used to define a +# list of protein domain databases, using three columns tab separated +# (longer whitespace are TAB characters): +# +# <unique_id>{tab}<database_caption>{tab}<base_name_path> # -#<unique_id> <database_caption> <base_name_path> +# The captions typically contain spaces and might end with the build date. +# It is important that the actual database name does not have a space in +# it, and that there are only two tabs on each line. +# +# You can download the NCBI provided databases as tar-balls from here: +# ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/ # -#The captions typically contain spaces and might end with the build date. -#It is important that the actual database name does not have a space in it, -#and that there are only two tabs on each line. +# For simplicity, many Galaxy servers are configured to offer just a live +# version of each NCBI BLAST database (updated with the NCBI provided +# Perl scripts or similar). In this case, we recommend using the case +# sensistive base-name of the NCBI BLAST databases as the unique id. +# Consistent naming is important for sharing workflows between Galaxy +# servers. # -#You can download the NCBI provided databases as tar-balls from here: -#ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/ +# For example, consider the NCBI Conserved Domains Database (CDD), where +# you have downloaded and decompressed the files under the directory +# /data/blastdb/domains/ meaning at the command line BLAST+ would be +# run as follows any would look at the files /data/blastdb/domains/Cdd.*: # -#So, for example, if your database is CDD and the path to your base name -#is /data/blastdb/Cdd, then the blastdb_d.loc entry would look like this: -# -#Cdd{tab}NCBI Conserved Domains Database (CDD){tab}/data/blastdb/Cdd +# $ rpsblast -db /data/blastdb/domains/Cdd -query ... # -#and your /data/blastdb directory would contain all of the files associated -#with the database, /data/blastdb/Cdd.*. +# In this case use Cdd (title case to match the NCBI file naming) as the +# unique id in the first column of blastdb_d.loc, giving an entry like +# this: # -#Your blastdb_d.loc file should include an entry per line for each "base name" -#you have stored. For example: +# Cdd{tab}NCBI Conserved Domains Database (CDD){tab}/data/blastdb/domains/Cdd +# +# Your blastdb_d.loc file should include an entry per line for each "base name" +# you have stored. For example: # -#Cdd NCBI CDD /data/blastdb/domains/Cdd -#Kog KOG (eukaryotes) /data/blastdb/domains/Kog -#Cog COG (prokaryotes) /data/blastdb/domains/Cog -#Pfam Pfam-A /data/blastdb/domains/Pfam -#Smart SMART /data/blastdb/domains/Smart -#Tigr TIGR /data/blastdb/domains/Tigr -#Prk Protein Clusters database /data/blastdb/domains/Prk -#...etc... +# Cdd{tab}NCBI CDD{tab}/data/blastdb/domains/Cdd +# Kog{tab}KOG (eukaryotes){tab}/data/blastdb/domains/Kog +# Cog{tab}COG (prokaryotes){tab}/data/blastdb/domains/Cog +# Pfam{tab}Pfam-A{tab}/data/blastdb/domains/Pfam +# Smart{tab}SMART{tab}/data/blastdb/domains/Smart +# Tigr{tab}TIGR /data/blastdb/domains/Tigr +# Prk{tab}Protein Clusters database{tab}/data/blastdb/domains/Prk +# ...etc... # -#See also blastdb.loc which is for any nucleotide BLAST database, and -#blastdb_p.loc which is for any protein BLAST databases. +# Alternatively, rather than a "live" mirror of the NCBI databases which +# are updated automatically, for full reproducibility the Galaxy Team +# recommend saving date-stamped copies of the databases. In this case +# your blastdb_d.loc file should include an entry per line for each +# version you have stored. For example: +# +# Cdd_05Jun2010{tab}NCBI CDD 05 Jun 2010{tab}/data/blastdb/domains/05Jun2010/Cdd +# Cdd_15Aug2010{tab}NCBI CDD 15 Aug 2010{tab}/data/blastdb/domains/15Aug2010/Cdd +# ...etc... +# +# See also blastdb.loc which is for any nucleotide BLAST database, and +# blastdb_p.loc which is for any protein BLAST databases. |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b tool-data/blastdb_p.loc.sample --- a/tool-data/blastdb_p.loc.sample Mon Dec 01 05:59:16 2014 -0500 +++ b/tool-data/blastdb_p.loc.sample Sun Jul 05 10:37:27 2015 -0400 |
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| @@ -1,30 +1,44 @@ -#This is a sample file distributed with Galaxy that is used to define a -#list of protein BLAST databases, using three columns tab separated -#(longer whitespace are TAB characters): +# This is a sample file distributed with Galaxy that is used to define a +# list of protein BLAST databases, using three columns tab separated: # -#<unique_id> <database_caption> <base_name_path> +# <unique_id>{tab}<database_caption>{tab}<base_name_path> +# +# The captions typically contain spaces and might end with the build date. +# It is important that the actual database name does not have a space in +# it, and that there are only two tabs on each line. # -#The captions typically contain spaces and might end with the build date. -#It is important that the actual database name does not have a space in -#it, and that there are only two tabs on each line. +# You can download the NCBI provided protein databases like NR from here: +# ftp://ftp.ncbi.nlm.nih.gov/blast/db/ # -#So, for example, if your database is NR and the path to your base name -#is /data/blastdb/nr, then the blastdb_p.loc entry would look like this: -# -#nr{tab}NCBI NR (non redundant){tab}/data/blastdb/nr +# For simplicity, many Galaxy servers are configured to offer just a live +# version of each NCBI BLAST database (updated with the NCBI provided +# Perl scripts or similar). In this case, we recommend using the case +# sensistive base-name of the NCBI BLAST databases as the unique id. +# Consistent naming is important for sharing workflows between Galaxy +# servers. # -#and your /data/blastdb directory would contain all of the files associated -#with the database, /data/blastdb/nr.*. +# For example, consider the NCBI "non-redundant" protein BLAST database +# where you have downloaded and decompressed the files under /data/blastdb/ +# meaning at the command line BLAST+ would be run with something like +# which would look at the files /data/blastdb/nr.p*: # -#Your blastdb_p.loc file should include an entry per line for each "base name" -#you have stored. For example: +# $ blastp -db /data/blastdb/nr -query ... +# +# In this case use nr (lower case to match the NCBI file naming) as the +# unique id in the first column of blastdb_p.loc, giving an entry like +# this: +# +# nr{tab}NCBI non-redundant (nr){tab}/data/blastdb/nr # -#nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010 /data/blastdb/05Jun2010/nr -#nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr -#...etc... +# Alternatively, rather than a "live" mirror of the NCBI databases which +# are updated automatically, for full reproducibility the Galaxy Team +# recommend saving date-stamped copies of the databases. In this case +# your blastdb_p.loc file should include an entry per line for each +# version you have stored. For example: # -#You can download the NCBI provided protein databases like NR from here: -#ftp://ftp.ncbi.nlm.nih.gov/blast/db/ +# nr_05Jun2010{tab}NCBI NR (non redundant) 05 Jun 2010{tab}/data/blastdb/05Jun2010/nr +# nr_15Aug2010{tab}NCBI NR (non redundant) 15 Aug 2010{tab}/data/blastdb/15Aug2010/nr +# ...etc... # -#See also blastdb.loc which is for any nucleotide BLAST database, and -#blastdb_d.loc which is for any protein domains databases (like CDD). +# See also blastdb.loc which is for any nucleotide BLAST database, and +# blastdb_d.loc which is for any protein domains databases (like CDD). |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b tool-data/tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/tool_data_table_conf.xml.sample Sun Jul 05 10:37:27 2015 -0400 |
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| @@ -0,0 +1,14 @@ +<tables> + <table name="blastdb" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/blastdb.loc" /> + </table> + <table name="blastdb_p" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/blastdb_p.loc" /> + </table> + <table name="blastdb_d" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/blastdb_d.loc" /> + </table> +</tables> |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b tools/ncbi_blast_plus/README.rst --- a/tools/ncbi_blast_plus/README.rst Mon Dec 01 05:59:16 2014 -0500 +++ b/tools/ncbi_blast_plus/README.rst Sun Jul 05 10:37:27 2015 -0400 |
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| @@ -7,7 +7,7 @@ See the licence text below. -Currently tested with NCBI BLAST 2.2.29+ (i.e. version 2.2.29 of BLAST+), +Currently tested with NCBI BLAST 2.2.30+ (i.e. version 2.2.30 of BLAST+), and does not work with the NCBI 'legacy' BLAST suite (e.g. ``blastall``). Note that these wrappers (and the associated datatypes) were originally @@ -19,6 +19,25 @@ These wrappers are available from the Galaxy Tool Shed at: http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus +In-development test releases are available from the Test Tool Shed at: +http://testtoolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/ + + +Citation +======== + +Please cite the following paper (currently available as a preprint): + +NCBI BLAST+ integrated into Galaxy. +P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo +bioRxiv DOI: http://dx.doi.org/10.1101/014043 (preprint) + +You should also cite the NCBI BLAST+ tools: + +BLAST+: architecture and applications. +C. Camacho et al. BMC Bioinformatics 2009, 10:421. +DOI: http://dx.doi.org/10.1186/1471-2105-10-421 + Automated Installation ====================== @@ -35,8 +54,7 @@ For those not using Galaxy's automated installation from the Tool Shed, put the XML and Python files in the ``tools/ncbi_blast_plus/`` folder and add the -XML files to your ``tool_conf.xml`` as normal (and do the same in -``tool_conf.xml.sample`` in order to run the unit tests). For example, use:: +XML files to your ``tool_conf.xml`` as normal. For example, use:: <section name="NCBI BLAST+" id="ncbi_blast_plus_tools"> <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" /> @@ -61,15 +79,16 @@ As described above for an automated installation, you must also tell Galaxy about any system level BLAST databases using the ``tool-data/blastdb*.loc`` -files. +files. Also merge the ``tool-data/tool_data_table_conf.xml.sample`` contents +into your ``tool_data_table_conf.xml`` file. You must install the NCBI BLAST+ standalone tools somewhere on the system -path. Currently the unit tests are written using BLAST 2.2.29+. +path. Currently the unit tests are written using BLAST+ 2.2.30. Run the functional tests (adjusting the section identifier to match your ``tool_conf.xml.sample`` file):: - ./run_functional_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools + ./run_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools Configuration ============= @@ -157,7 +176,7 @@ - Set number of threads via ``$GALAXY_SLOTS`` environment variable. - More descriptive default output names. - Tests require updated BLAST DB definitions (``blast_datatypes`` v0.0.18). - - Pre-check for duplicate identifiers in makeblastdb wrapper. + - Pre-check for duplicate identifiers in ``makeblastdb`` wrapper. - Tests updated for BLAST+ 2.2.28 instead of BLAST+ 2.2.27. - Now depends on ``package_blast_plus_2_2_28`` in ToolShed. - Extended tabular output includes 'salltitles' as column 25. @@ -170,8 +189,8 @@ - More detailed descriptions for BLASTN and BLASTP task option. - Wrappers for segmasker, dustmasker and convert2blastmask (contribution from Bjoern Gruening). - - Supports using maskinfo with makeblastdb wrapper. - - Supports setting a taxonomy ID in makeblastdb wrapper. + - Supports using maskinfo with ``makeblastdb`` wrapper. + - Supports setting a taxonomy ID in ``makeblastdb`` wrapper. - Subtle changes like new conditional settings will require some old workflows be updated to cope. v0.1.01 - Requires ``blastdbd`` datatype (``blast_datatypes`` v0.0.19). @@ -181,6 +200,21 @@ domain database from the user's history. - Tool definitions now embed citation information (by John Chilton). - BLAST tools support GI and SeqID filters (added by Bjoern Gruening). +v0.1.02 - Now depends on ``package_blast_plus_2_2_30`` in ToolShed. + - Tests updated for BLAST+ 2.2.30 instead of BLAST+ 2.2.29. + - New tasks ``blastp-fast``, ``blastx-fast`` and ``tblastn-fast``. + - New minimum query HSP coverage option, ``-qcov_hsp_perc``. + - Removed ``-word_size`` from RPS-BLAST and RPS-TBLASTN wrappers, this + is set during database construction and should not have been offered + as a command line option in releases prior to BLAST+ 2.2.30. + - BLAST database ``blastdb*.loc`` files now accessed via the XML + table definitions in Galaxy's ``tool_data_table_conf.xml`` file, + setup via ``tool-data/tool_data_table_conf.xml.sample`` + - Replace ``.extra_files_path`` with ``.files_path`` (internal change, + thanks to Bjoern Gruening and John Chilton). + - Added "NCBI BLAST+ integrated into Galaxy" preprint citation. +v0.1.03 - Reorder XML elements (internal change only). + - Planemo for Tool Shed upload (``.shed.yml``, internal change only). ======= ====================================================================== @@ -201,10 +235,28 @@ As of July 2013, development is continuing on a dedicated GitHub repository: https://github.com/peterjc/galaxy_blast -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use -the following command from the GitHub repository root folder:: +For pushing a release to the test or main "Galaxy Tool Shed", use the following +Planemo commands (which requires you have set your Tool Shed access details in +``~/.planemo.yml`` and that you have access rights on the Tool Shed):: + + $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/galaxy_blast/tools/ncbi_blast_plus/ + ... + +or:: - $ tools/ncbi_blast_plus/make_ncbi_blast_plus.sh + $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/galaxy_blast/tools/ncbi_blast_plus/ + ... + +To just build and check the tar ball, use:: + + $ planemo shed_upload --tar_only ~/repositories/galaxy_blast/tools/ncbi_blast_plus/ + ... + $ tar -tzf shed_upload.tar.gz + test-data/blastdb.loc + ... + tools/ncbi_blast_plus/tool_dependencies.xml + $ tar -tzf shed_upload.tar.gz | wc -l + 117 This simplifies ensuring a consistent set of files is bundled each time, including all the relevant test files. |
| b |
| diff -r 2fe07f50a41e -r c16c30e9ad5b tools/ncbi_blast_plus/blastxml_to_tabular.py --- a/tools/ncbi_blast_plus/blastxml_to_tabular.py Mon Dec 01 05:59:16 2014 -0500 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py Sun Jul 05 10:37:27 2015 -0400 |
| [ |
| @@ -1,9 +1,9 @@ #!/usr/bin/env python """Convert a BLAST XML file to tabular output. -Takes three command line options, input BLAST XML filename, output tabular -BLAST filename, output format (std for standard 12 columns, or ext for the -extended 24 columns offered in the BLAST+ wrappers). +Designed to convert BLAST XML files into tabular BLAST output (either +std for standard 12 columns, or ext for the extended 25 columns offered +in the Galaxy BLAST+ wrappers). The 12 columns output are 'qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore' or 'std' at the BLAST+ command line, which @@ -66,7 +66,7 @@ from optparse import OptionParser if "-v" in sys.argv or "--version" in sys.argv: - print "v0.1.01" + print "v0.1.04" sys.exit(0) if sys.version_info[:2] >= ( 2, 5 ): @@ -162,7 +162,7 @@ blast_program = None # get an iterable try: - context = ElementTree.iterparse(in_file, events=("start", "end")) + context = ElementTree.iterparse(blastxml_filename, events=("start", "end")) except: stop_err("Invalid data format.") # turn it into an iterator @@ -321,7 +321,7 @@ #Only a subset of the columns are needed values = [values[colnames.index(c)] for c in cols] #print "\t".join(values) - outfile.write("\t".join(values) + "\n") + output_handle.write("\t".join(values) + "\n") # prevents ElementTree from growing large datastructure root.clear() elem.clear() |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b tools/ncbi_blast_plus/blastxml_to_tabular.xml --- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml Mon Dec 01 05:59:16 2014 -0500 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml Sun Jul 05 10:37:27 2015 -0400 |
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| @@ -1,5 +1,10 @@ -<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.1.01"> +<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.1.05"> <description>Convert BLAST XML output to tabular</description> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> <version_command interpreter="python">blastxml_to_tabular.py --version</version_command> <command interpreter="python"> blastxml_to_tabular.py -o "$tabular_file" @@ -9,13 +14,8 @@ #else -c "$output.out_format" #end if -#for i in $blastxml_file#${i} #end for# +#for i in $blastxml_file#"${i}" #end for# </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> <inputs> <param name="blastxml_file" type="data" format="blastxml" multiple="true" label="BLAST results as XML"/> <conditional name="output"> @@ -62,8 +62,6 @@ <outputs> <data name="tabular_file" format="tabular" label="$on_string (as tabular)" /> </outputs> - <requirements> - </requirements> <tests> <test> <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Mon Dec 01 05:59:16 2014 -0500 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Sun Jul 05 10:37:27 2015 -0400 |
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| @@ -1,20 +1,34 @@ -<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.1.01"> +<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.1.03"> <description>Show BLAST database information from blastdbcmd</description> <macros> <token name="@BINARY@">blastdbcmd</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="preamble" /> <command> blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}" -info -out "$info" </command> - <expand macro="stdio" /> <inputs> <expand macro="input_conditional_choose_db_type" /> </inputs> <outputs> <data name="info" format="txt" label="${db_opts.database.fields.name} info" /> </outputs> + <tests> + <!-- Disable for ToolShed where *.loc tests not yet supported + See https://github.com/peterjc/galaxy_blast/issues/53 + <test> + <param name="db_opts|db_type" value="prot" /> + <param name="db_opts|database" value="four_human_proteins" /> + <output name="info" file="four_human_proteins.dbinfo.txt" ftype="txt" lines_diff="4" /> + </test> + <test> + <param name="db_opts|db_type" value="nucl" /> + <param name="db_opts|database" value="three_human_mRNA" /> + <output name="info" file="three_human_mRNA.dbinfo.txt" ftype="txt" lines_diff="4" /> + </test> + --> + </tests> <help> **What it does** |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Mon Dec 01 05:59:16 2014 -0500 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Sun Jul 05 10:37:27 2015 -0400 |
| [ |
| @@ -1,10 +1,10 @@ -<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.1.01"> +<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.1.03"> <description>Extract sequence(s) from BLAST database</description> <macros> <token name="@BINARY@">blastdbcmd</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="preamble" /> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces @@ -47,7 +47,6 @@ | sed 's/>\(lcl|\|gnl|BL_ORD_ID|[0-9]* \)/>/1' > "$seq" #end if </command> - <expand macro="stdio" /> <inputs> <expand macro="input_conditional_choose_db_type" /> <conditional name="id_opts"> @@ -70,6 +69,19 @@ <outputs> <data name="seq" format="fasta" label="Sequences from ${db_opts.database.fields.name}" /> </outputs> + <tests> + <!-- Disable for ToolShed where *.loc tests not yet supported + See https://github.com/peterjc/galaxy_blast/issues/53 + <test> + <param name="db_opts|db_type" value="prot" /> + <param name="db_opts|database" value="four_human_proteins" /> + <param name="id_opts|id_type" value="prompt" /> + <param name="id_opts|entries" value="all" /> + <param name="outfmt" value="original" /> + <output name="seq" file="four_human_proteins.fasta" ftype="fasta" /> + </test> + --> + </tests> <help> **What it does** |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Mon Dec 01 05:59:16 2014 -0500 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Sun Jul 05 10:37:27 2015 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.1.01"> +<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.1.03"> <description>Search nucleotide database with nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism> @@ -6,7 +6,7 @@ <token name="@BINARY@">blastn</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="preamble" /> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces @@ -19,23 +19,21 @@ @THREADS@ #if $adv_opts.adv_opts_selector=="advanced": $adv_opts.strand -@ADVANCED_OPTIONS@ +@ADV_FILTER_QUERY@ +@ADV_MAX_HITS@ +@ADV_WORD_SIZE@ #if (str($adv_opts.identity_cutoff) and float(str($adv_opts.identity_cutoff)) > 0 ): -perc_identity $adv_opts.identity_cutoff #end if $adv_opts.ungapped @ADV_ID_LIST_FILTER@ +@ADV_QCOV_HSP_PERC@ ## End of advanced options: #end if </command> - - <expand macro="stdio" /> - <inputs> <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> - <expand macro="input_conditional_nucleotide_db" /> - <param name="blast_type" type="select" display="radio" label="Type of BLAST"> <option value="megablast">megablast - Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequences</option> <option value="blastn">blastn - Traditional BLASTN requiring an exact match of 11, for somewhat similar sequences</option> @@ -64,6 +62,7 @@ <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> <expand macro="input_parse_deflines" /> <expand macro="advanced_optional_id_files" /> + <expand macro="input_qcov_hsp_perc" /> </expand> </inputs> <outputs> @@ -104,6 +103,27 @@ <param name="adv_opts_selector" value="basic" /> <output name="output1" file="blastn_rhodopsin_vs_three_human.columns.tabular" ftype="tabular" /> </test> + <!-- Disable for ToolShed where *.loc tests not yet supported + See https://github.com/peterjc/galaxy_blast/issues/53 + <test> + <param name="query" value="chimera.fasta" ftype="fasta" /> + <param name="db_opts_selector" value="db" /> + <param name="database" value="three_human_mRNA" /> + <param name="out_format" value="6" /> + <param name="adv_opts_selector" value="advanced" /> + <param name="max_hits" value="1" /> + <output name="output1" file="blastn_chimera_vs_three_human_max1.tabular" ftype="tabular" /> + </test> + <test> + <param name="query" value="chimera.fasta" ftype="fasta" /> + <param name="db_opts_selector" value="db" /> + <param name="database" value="three_human_mRNA" /> + <param name="out_format" value="0" /> + <param name="adv_opts_selector" value="advanced" /> + <param name="max_hits" value="1" /> + <output name="output1" file="blastn_chimera_vs_three_human_max1.txt" ftype="txt" /> + </test> + --> </tests> <help> |
| b |
| diff -r 2fe07f50a41e -r c16c30e9ad5b tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Mon Dec 01 05:59:16 2014 -0500 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Sun Jul 05 10:37:27 2015 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.1.01"> +<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.1.03"> <description>Search protein database with protein query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1" /> @@ -6,7 +6,7 @@ <token name="@BINARY@">blastp</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="preamble" /> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces @@ -19,16 +19,16 @@ @THREADS@ #if $adv_opts.adv_opts_selector=="advanced": -matrix $adv_opts.matrix -@ADVANCED_OPTIONS@ +@ADV_FILTER_QUERY@ +@ADV_MAX_HITS@ +@ADV_WORD_SIZE@ ##Ungapped disabled for now - see comments below ##$adv_opts.ungapped @ADV_ID_LIST_FILTER@ +@ADV_QCOV_HSP_PERC@ ## End of advanced options: #end if </command> - - <expand macro="stdio" /> - <inputs> <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> @@ -36,6 +36,7 @@ <param name="blast_type" type="select" display="radio" label="Type of BLAST"> <option value="blastp">blastp - Traditional BLASTP to compare a protein query to a protein database</option> + <option value="blastp-fast">blastp-fast - Use longer words for seeding, faster but less accurate</option> <option value="blastp-short">blastp-short - BLASTP optimized for queries shorter than 30 residues</option> </param> <expand macro="input_evalue" /> @@ -54,6 +55,7 @@ --> <expand macro="input_parse_deflines" /> <expand macro="advanced_optional_id_files" /> + <expand macro="input_qcov_hsp_perc" /> </expand> </inputs> <outputs> @@ -76,6 +78,7 @@ <param name="max_hits" value="0" /> <param name="word_size" value="0" /> <param name="parse_deflines" value="True" /> + <param name="qcov_hsp_perc" value="25" /> <output name="output1" file="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> </test> <test> @@ -92,6 +95,7 @@ <param name="max_hits" value="0" /> <param name="word_size" value="0" /> <param name="parse_deflines" value="True" /> + <param name="qcov_hsp_perc" value="25" /> <output name="output1" file="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" /> </test> <test> @@ -108,6 +112,7 @@ <param name="max_hits" value="0" /> <param name="word_size" value="0" /> <param name="parse_deflines" value="True" /> + <param name="qcov_hsp_perc" value="25" /> <output name="output1" file="blastp_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" /> </test> <test> |
| b |
| diff -r 2fe07f50a41e -r c16c30e9ad5b tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Mon Dec 01 05:59:16 2014 -0500 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Sun Jul 05 10:37:27 2015 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.1.01"> +<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.1.03"> <description>Search protein database with translated nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism> @@ -6,7 +6,7 @@ <token name="@BINARY@">blastx</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="preamble" /> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces @@ -14,26 +14,31 @@ -query "$query" @BLAST_DB_SUBJECT@ -query_gencode $query_gencode +-task $blast_type -evalue $evalue_cutoff @BLAST_OUTPUT@ @THREADS@ #if $adv_opts.adv_opts_selector=="advanced": $adv_opts.strand -matrix $adv_opts.matrix -@ADVANCED_OPTIONS@ +@ADV_FILTER_QUERY@ +@ADV_MAX_HITS@ +@ADV_WORD_SIZE@ $adv_opts.ungapped @ADV_ID_LIST_FILTER@ +@ADV_QCOV_HSP_PERC@ ## End of advanced options: #end if </command> - - <expand macro="stdio" /> - <inputs> <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> <expand macro="input_conditional_protein_db" /> <expand macro="input_query_gencode" /> + <param name="blast_type" type="select" display="radio" label="Type of BLAST"> + <option value="blastx">blastx - Traditional BLASTX to compare translated nucleotide query to protein database</option> + <option value="blastx-fast">blastx-fast - Use longer words for seeding, faster but less accurate</option> + </param> <expand macro="input_evalue" /> <expand macro="input_out_format" /> @@ -47,6 +52,7 @@ <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> <expand macro="input_parse_deflines" /> <expand macro="advanced_optional_id_files" /> + <expand macro="input_qcov_hsp_perc" /> </expand> </inputs> <outputs> |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml Mon Dec 01 05:59:16 2014 -0500 +++ b/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml Sun Jul 05 10:37:27 2015 -0400 |
| b |
| @@ -1,10 +1,10 @@ -<tool id="ncbi_convert2blastmask_wrapper" name="NCBI BLAST+ convert2blastmask" version="0.1.01"> +<tool id="ncbi_convert2blastmask_wrapper" name="NCBI BLAST+ convert2blastmask" version="0.1.03"> <description>Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb</description> <macros> <token name="@BINARY@">convert2blastmask</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="preamble" /> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces @@ -16,7 +16,6 @@ -out "$outfile" -outfmt $outformat </command> - <expand macro="stdio" /> <inputs> <param name="infile" type="data" format="fasta" label="masked FASTA file"/> <param name="masking_algorithm" type="select" label="Used masking algorithm"> @@ -80,7 +79,7 @@ **References** If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers (a more specific paper covering this wrapper is planned): +cite the following papers: @REFERENCES@ </help> |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Mon Dec 01 05:59:16 2014 -0500 +++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Sun Jul 05 10:37:27 2015 -0400 |
| b |
| @@ -1,11 +1,11 @@ -<tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="0.1.01"> +<tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="0.1.03"> <!-- dustmasker wrapper from Edward Kirton and Nicola Soranzo --> <description>masks low complexity regions</description> <macros> <token name="@BINARY@">dustmasker</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="preamble" /> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces @@ -13,14 +13,13 @@ #if $db_opts.db_opts_selector == "db": -in "${db_opts.database.fields.path}" -infmt blastdb #elif $db_opts.db_opts_selector == "histdb": - -in "${os.path.join($db_opts.histdb.extra_files_path, 'blastdb')}" -infmt blastdb + -in "${os.path.join($db_opts.histdb.files_path, 'blastdb')}" -infmt blastdb #else: -in "$subject" -infmt fasta #end if -out "$outfile" -window $window -level $level -linker $linker -outfmt $outformat </command> - <expand macro="stdio" /> <inputs> <expand macro="input_conditional_nucleotide_db" /> <param name="window" type="integer" value="64" label="DUST window length" /> @@ -92,7 +91,7 @@ **References** If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers (a more specific paper covering this wrapper is planned): +cite the following papers: @REFERENCES@ </help> |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b tools/ncbi_blast_plus/ncbi_macros.xml --- a/tools/ncbi_blast_plus/ncbi_macros.xml Mon Dec 01 05:59:16 2014 -0500 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Sun Jul 05 10:37:27 2015 -0400 |
| [ |
| b'@@ -1,4 +1,20 @@\n <macros>\n+ <xml name="preamble">\n+ <requirements>\n+ <requirement type="binary">@BINARY@</requirement>\n+ <requirement type="package" version="2.2.30">blast+</requirement>\n+ </requirements>\n+ <stdio>\n+ <!-- Anything other than zero is an error -->\n+ <exit_code range="1:" />\n+ <!-- Might see negative return codes for Unix signals via Python subprocess -->\n+ <exit_code range=":-1" />\n+ <!-- In case the return code has not been set properly check stderr too -->\n+ <regex match="Error:" />\n+ <regex match="Exception:" />\n+ </stdio>\n+ <version_command>@BINARY@ -version</version_command>\n+ </xml>\n <xml name="output_change_format">\n <change_format>\n <when input="output.out_format" value="0" format="txt"/>\n@@ -59,7 +75,7 @@\n <option value="slen">slen = Subject sequence length</option>\n <option value="salltitles">salltitles = All subject title(s), separated by a \'<>\'</option>\n </param>\n- <param name="ids_cols" type="select" multiple="true" display="checkboxes" label="Other identifer columns">\n+ <param name="ids_cols" type="select" multiple="true" display="checkboxes" label="Other identifier columns">\n <option value="qgi">qgi = Query GI</option>\n <option value="qacc">qacc = Query accesion</option>\n <option value="qaccver">qaccver = Query accesion.version</option>\n@@ -109,17 +125,6 @@\n <option value="PAM30">PAM30</option>\n </param>\n </xml>\n- <xml name="stdio">\n- <stdio>\n- <!-- Anything other than zero is an error -->\n- <exit_code range="1:" />\n- <!-- Might see negative return codes for Unix signals via Python subprocess -->\n- <exit_code range=":-1" />\n- <!-- In case the return code has not been set properly check stderr too -->\n- <regex match="Error:" />\n- <regex match="Exception:" />\n- </stdio>\n- </xml>\n <xml name="input_query_gencode">\n <param name="query_gencode" type="select" label="Query genetic code">\n <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->\n@@ -175,11 +180,7 @@\n </param>\n <when value="db">\n <param name="database" type="select" label="Nucleotide BLAST database">\n- <options from_file="blastdb.loc">\n- <column name="value" index="0"/>\n- <column name="name" index="1"/>\n- <column name="path" index="2"/>\n- </options>\n+ <options from_data_table="blastdb" />\n </param>\n <param name="histdb" type="hidden" value="" />\n <param name="subject" type="hidden" value="" /> \n@@ -205,11 +206,7 @@\n </param>\n <when value="db">\n <param name="database" type="select" label="Protein BLAST database">\n- <options from_file="blastdb_p.loc">\n- <column name="value" index="0"/>\n- <column name="name" index="1"/>\n- <column name="path" index="2"/>\n- </options>\n+ <options from_data_table="blastdb_p" />\n </param>\n <param name="histdb" type="hidden" value="" />\n <param name="subject" type="hidden" value="" />\n@@ -234,11 +231,7 @@\n </param>\n <when value="db">\n <param name="database" type="select" label="Protein domain database">\n- <options from_file="blastdb_d.loc">\n- <column name="value" index="0"/>\n- <column name="name" index="1"/>\n- '..b'ion value="none" selected="True">No restriction, search the entire database</option>\n- <option value="gilist">GI identifers</option>\n- <option value="negative_gilist">Negative GI identifers</option>\n- <option value="seqidlist">Sequence identifers (SeqId\'s)</option>\n+ <option value="gilist">GI identifiers</option>\n+ <option value="negative_gilist">Negative GI identifiers</option>\n+ <option value="seqidlist">Sequence identifiers (SeqId\'s)</option>\n </param>\n <when value="none" />\n <when value="gilist">\n@@ -349,6 +330,11 @@\n </when>\n </conditional>\n </xml>\n+ <token name="@ADV_QCOV_HSP_PERC@">\n+#if float(str($adv_opts.qcov_hsp_perc)) > 0:\n+ -qcov_hsp_perc $adv_opts.qcov_hsp_perc\n+#end if\n+ </token>\n <token name="@ADV_ID_LIST_FILTER@">\n #if $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == \'negative_gilist\':\n -negative_gilist $adv_opts.adv_optional_id_files_opts.negative_gilist\n@@ -363,7 +349,7 @@\n #if $db_opts.db_opts_selector == "db":\n -db "${db_opts.database.fields.path}"\n #elif $db_opts.db_opts_selector == "histdb":\n- -db "${os.path.join($db_opts.histdb.extra_files_path,\'blastdb\')}"\n+ -db "${os.path.join($db_opts.histdb.files_path,\'blastdb\')}"\n #else:\n -subject "$db_opts.subject"\n #end if\n@@ -381,12 +367,22 @@\n -outfmt $output.out_format\n #end if\n </token>\n- <token name="@ADVANCED_OPTIONS@">$adv_opts.filter_query\n+ <token name="@ADV_FILTER_QUERY@">$adv_opts.filter_query</token>\n+ <token name="@ADV_MAX_HITS@">\n ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string\n-## Note -max_target_seqs overrides -num_descriptions and -num_alignments\n+## Note -max_target_seqs used to simply override -num_descriptions and -num_alignments\n+## but this was changed in BLAST+ 2.2.27 onwards to force their use (raised with NCBI)\n #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):\n+#if str($output.out_format) in ["6", "ext", "cols", "5"]:\n+## Most output formats use this, including tabular and XML:\n -max_target_seqs $adv_opts.max_hits\n+#else\n+## Text and HTML output formats 0-4 currently need this instead:\n+-num_descriptions $adv_opts.max_hits -num_alignments $adv_opts.max_hits\n #end if\n+#end if\n+ </token>\n+ <token name="@ADV_WORD_SIZE@">\n #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):\n -word_size $adv_opts.word_size\n #end if\n@@ -401,14 +397,18 @@\n ${db_opts.subject.name}\n #end if</token>\n <token name="@REFERENCES@">\n+Peter J. A. Cock, John M. Chilton, Bj\xc3\xb6rn Gr\xc3\xbcning, James E. Johnson, Nicola Soranzo (2015).\n+NCBI BLAST+ integrated into Galaxy. *BioRxiv* preprint.\n+http://dx.doi.org/10.1101/014043\n+\n Peter J.A. Cock, Bj\xc3\xb6rn A. Gr\xc3\xbcning, Konrad Paszkiewicz and Leighton Pritchard (2013).\n Galaxy tools and workflows for sequence analysis with applications\n-in molecular plant pathology. PeerJ 1:e167\n+in molecular plant pathology. *PeerJ* 1:e167\n http://dx.doi.org/10.7717/peerj.167\n \n Christiam Camacho et al. (2009).\n BLAST+: architecture and applications.\n-BMC Bioinformatics. 15;10:421.\n+*BMC Bioinformatics*. 15;10:421.\n http://dx.doi.org/10.1186/1471-2105-10-421\n \n This wrapper is available to install into other Galaxy Instances via the Galaxy\n@@ -418,7 +418,9 @@\n <citations>\n <citation type="doi">10.1186/1471-2105-10-421</citation>\n <citation type="doi">10.7717/peerj.167</citation>\n- <!-- TODO: Add BibTeX entry / preprint DOI for Galaxy BLAST+ paper -->\n+ <!-- TODO - remove PeerJ paper once "NCBI BLAST+ integrated into Galaxy" formally published? -->\n+ <citation type="doi">10.1101/014043</citation>\n+ <!-- TODO - Update DOI once "NCBI BLAST+ integrated into Galaxy" formally published -->\n </citations>\n </xml>\n <token name="@OUTPUT_FORMAT@">**Output format**\n' |
| b |
| diff -r 2fe07f50a41e -r c16c30e9ad5b tools/ncbi_blast_plus/ncbi_makeblastdb.xml --- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Mon Dec 01 05:59:16 2014 -0500 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Sun Jul 05 10:37:27 2015 -0400 |
| b |
| @@ -1,16 +1,16 @@ -<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.1.01"> +<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.1.03"> <description>Make BLAST database</description> <macros> <token name="@BINARY@">makeblastdb</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="preamble" /> <command interpreter="python">check_no_duplicates.py ##First check for duplicates (since BLAST+ 2.2.28 fails to do so) ##and abort (via the ampersand ampersand trick) if any are found. #for i in $input_file#"${i}" #end for# && -makeblastdb -out "${os.path.join($outfile.extra_files_path,'blastdb')}" +makeblastdb -out "${os.path.join($outfile.files_path,'blastdb')}" $parse_seqids $hash_index ## Single call to -in with multiple filenames space separated with outer quotes @@ -47,7 +47,6 @@ ## Capture the stdout log information to the primary file (plain text): > "$outfile" </command> - <expand macro="stdio" /> <inputs> <param name="dbtype" type="select" display="radio" label="Molecule type of input"> <option value="prot">protein</option> @@ -97,6 +96,7 @@ </outputs> <tests> <!-- Note the (two line) PIN file is not reproducible run to run. + The same applies to the NIN file for nucleotide database. Likewise there is a datestamp in the log file as well, so use contains comparison With and without the masking makes no difference. With and without the taxid the only real difference is in the *.phr file. @@ -155,6 +155,25 @@ <extra_files type="file" value="four_human_proteins.fasta.psi" name="blastdb.psi" /> </output> </test> + <test> + <param name="dbtype" value="nucl" /> + <param name="input_file" value="three_human_mRNA.fasta" ftype="fasta" /> + <param name="title" value="Just 3 human mRNA sequences" /> + <param name="parse_seqids" value="" /> + <param name="hash_index" value="true" /> + <param name="taxselect" value="id" /> + <param name="taxid" value="9606" /> + <output name="out_file" compare="contains" file="three_human_mRNA.fasta.log.txt" ftype="blastdbn"> + <extra_files type="file" value="three_human_mRNA.fasta.nhr" name="blastdb.nhr" /> + <extra_files type="file" value="three_human_mRNA.fasta.nin" name="blastdb.nin" lines_diff="2" /> + <extra_files type="file" value="three_human_mRNA.fasta.nsq" name="blastdb.nsq" /> + <extra_files type="file" value="three_human_mRNA.fasta.nog" name="blastdb.nog" /> + <extra_files type="file" value="three_human_mRNA.fasta.nhd" name="blastdb.nhd" /> + <extra_files type="file" value="three_human_mRNA.fasta.nhi" name="blastdb.nhi" /> + <extra_files type="file" value="three_human_mRNA.fasta.nsd" name="blastdb.nsd" /> + <extra_files type="file" value="three_human_mRNA.fasta.nsi" name="blastdb.nsi" /> + </output> + </test> </tests> <help> **What it does** |
| b |
| diff -r 2fe07f50a41e -r c16c30e9ad5b tools/ncbi_blast_plus/ncbi_makeprofiledb.xml --- a/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Mon Dec 01 05:59:16 2014 -0500 +++ b/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Sun Jul 05 10:37:27 2015 -0400 |
| b |
| @@ -1,14 +1,14 @@ -<tool id="ncbi_makeprofiledb" name="NCBI BLAST+ makeprofiledb" version="0.1.01"> +<tool id="ncbi_makeprofiledb" name="NCBI BLAST+ makeprofiledb" version="0.1.03"> <description>Make profile database</description> <macros> <token name="@BINARY@">makeprofiledb</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="preamble" /> <command> ##Unlike makeblastdb, makeprofiledb needs directory to exist already: -mkdir -p $outfile.extra_files_path && -makeprofiledb -out "${os.path.join($outfile.extra_files_path,'blastdb')}" +mkdir -p $outfile.files_path && +makeprofiledb -out "${os.path.join($outfile.files_path,'blastdb')}" ##We turn $infile_list into $infiles with a configfile entry defined below -in $infiles @@ -34,7 +34,13 @@ -logfile "$outfile" </command> - <expand macro="stdio" /> + <configfiles> + <configfile name="infiles"> +#for $infile in $input_file +${infile} +#end for + </configfile> + </configfiles> <inputs> <param name="input_file" type="data" multiple="true" optional="false" format="pssm-asn1" label="Input PSSM files(s)" @@ -75,13 +81,6 @@ label="Observation threshold" help="Exclude domains with with maximum number of independent observations below this threshold" /> </inputs> - <configfiles> - <configfile name="infiles"> -#for $infile in $input_file -${infile} -#end for - </configfile> - </configfiles> <outputs> <data name="outfile" format="blastdbd" label="RPS database from ${on_string}" /> </outputs> |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Mon Dec 01 05:59:16 2014 -0500 +++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Sun Jul 05 10:37:27 2015 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="0.1.01"> +<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="0.1.03"> <description>Search protein domain database (PSSMs) with protein query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1" /> @@ -6,7 +6,7 @@ <token name="@BINARY@">deltablast</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="preamble" /> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces @@ -15,19 +15,18 @@ #if $db_opts.db_opts_selector == "db": -db "${db_opts.database.fields.path}" #elif $db_opts.db_opts_selector == "histdb": - -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}" + -db "${os.path.join($db_opts.histdb.files_path,'blastdb')}" #end if -evalue $evalue_cutoff @BLAST_OUTPUT@ @THREADS@ #if $adv_opts.adv_opts_selector=="advanced": -@ADVANCED_OPTIONS@ +@ADV_FILTER_QUERY@ +@ADV_MAX_HITS@ +@ADV_QCOV_HSP_PERC@ ## End of advanced options: #end if </command> - - <expand macro="stdio" /> - <inputs> <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> @@ -41,8 +40,8 @@ <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> <expand macro="input_filter_query_default_false" /> <expand macro="input_max_hits" /> - <expand macro="input_word_size" /> <expand macro="input_parse_deflines" /> + <expand macro="input_qcov_hsp_perc" /> </expand> </inputs> <outputs> @@ -52,6 +51,19 @@ </data> </outputs> + <tests> + <!-- Disable for ToolShed where *.loc tests not yet supported + See https://github.com/peterjc/galaxy_blast/issues/53 + <test> + <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="db_opts_selector" value="db" /> + <param name="database" value="cd00003_and_cd00008" /> + <param name="evalue_cutoff" value="1e-8" /> + <param name="out_format" value="6" /> + <output name="output1" file="empty_file.dat" ftype="tabular" /> + </test> + --> + </tests> <help> @SEARCH_TIME_WARNING@ |
| b |
| diff -r 2fe07f50a41e -r c16c30e9ad5b tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Mon Dec 01 05:59:16 2014 -0500 +++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Sun Jul 05 10:37:27 2015 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="0.1.01"> +<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="0.1.03"> <description>Search protein domain database (PSSMs) with translated nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism> @@ -6,7 +6,7 @@ <token name="@BINARY@">rpstblastn</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="preamble" /> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces @@ -15,18 +15,19 @@ #if $db_opts.db_opts_selector == "db": -db "${db_opts.database.fields.path}" #elif $db_opts.db_opts_selector == "histdb": - -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}" + -db "${os.path.join($db_opts.histdb.files_path,'blastdb')}" #end if -evalue $evalue_cutoff @BLAST_OUTPUT@ ## rpstblastn does not support multiple threads up to release 2.2.27+. Added in BLAST 2.2.28+. ##-num_threads 8 #if $adv_opts.adv_opts_selector=="advanced": -@ADVANCED_OPTIONS@ +@ADV_FILTER_QUERY@ +@ADV_MAX_HITS@ +@ADV_QCOV_HSP_PERC@ ## End of advanced options: #end if </command> - <expand macro="stdio" /> <inputs> <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> @@ -41,8 +42,8 @@ <expand macro="input_filter_query_default_false" /> <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> <expand macro="input_max_hits" /> - <expand macro="input_word_size" /> <expand macro="input_parse_deflines" /> + <expand macro="input_qcov_hsp_perc" /> </expand> </inputs> <outputs> @@ -50,6 +51,19 @@ <expand macro="output_change_format" /> </data> </outputs> + <tests> + <!-- Disable for ToolShed where *.loc tests not yet supported + See https://github.com/peterjc/galaxy_blast/issues/53 + <test> + <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> + <param name="db_opts_selector" value="db" /> + <param name="database" value="cd00003_and_cd00008" /> + <param name="evalue_cutoff" value="1e-8" /> + <param name="out_format" value="6" /> + <output name="output1" file="empty_file.dat" ftype="tabular" /> + </test> + --> + </tests> <help> @SEARCH_TIME_WARNING@ |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml Mon Dec 01 05:59:16 2014 -0500 +++ b/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml Sun Jul 05 10:37:27 2015 -0400 |
| b |
| @@ -1,10 +1,10 @@ -<tool id="ncbi_segmasker_wrapper" name="NCBI BLAST+ segmasker" version="0.1.01"> +<tool id="ncbi_segmasker_wrapper" name="NCBI BLAST+ segmasker" version="0.1.03"> <description>low-complexity regions in protein sequences</description> <macros> <token name="@BINARY@">segmasker</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="preamble" /> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces @@ -12,7 +12,7 @@ #if $db_opts.db_opts_selector == "db": -in "${db_opts.database.fields.path}" -infmt blastdb #elif $db_opts.db_opts_selector == "histdb": - -in "${os.path.join($db_opts.histdb.extra_files_path, 'blastdb')}" -infmt blastdb + -in "${os.path.join($db_opts.histdb.files_path, 'blastdb')}" -infmt blastdb #else: -in "$subject" -infmt fasta #end if @@ -22,7 +22,6 @@ -hicut $hicut -outfmt $outformat </command> - <expand macro="stdio" /> <inputs> <expand macro="input_conditional_protein_db" /> <param name="window" type="integer" value="12" label="SEG window length" help="(-window)" /> @@ -94,7 +93,7 @@ **References** If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers (a more specific paper covering this wrapper is planned): +cite the following papers: @REFERENCES@ </help> |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Mon Dec 01 05:59:16 2014 -0500 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Sun Jul 05 10:37:27 2015 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.1.01"> +<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.1.03"> <description>Search translated nucleotide database with protein query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism> @@ -6,35 +6,40 @@ <token name="@BINARY@">tblastn</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="preamble" /> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces tblastn -query "$query" @BLAST_DB_SUBJECT@ +-task $blast_type -evalue $evalue_cutoff @BLAST_OUTPUT@ @THREADS@ #if $adv_opts.adv_opts_selector=="advanced": -db_gencode $adv_opts.db_gencode -matrix $adv_opts.matrix -@ADVANCED_OPTIONS@ +@ADV_FILTER_QUERY@ +@ADV_MAX_HITS@ +@ADV_WORD_SIZE@ ##Ungapped disabled for now - see comments below ##$adv_opts.ungapped @ADV_ID_LIST_FILTER@ +@ADV_QCOV_HSP_PERC@ ## End of advanced options: #end if </command> - - <expand macro="stdio" /> - <inputs> <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> <expand macro="input_conditional_nucleotide_db" /> + <param name="blast_type" type="select" display="radio" label="Type of BLAST"> + <option value="tblastn">tblastn - Traditional TBLASTN to compare protein query to translated nucleotide database</option> + <option value="tblastn-fast">tblastn-fast - Use longer words for seeding, faster but less accurate</option> + </param> + <expand macro="input_evalue" /> <expand macro="input_out_format" /> - <expand macro="input_evalue" /> <expand macro="advanced_options"> <expand macro="input_db_gencode" /> @@ -51,6 +56,7 @@ --> <expand macro="input_parse_deflines" /> <expand macro="advanced_optional_id_files" /> + <expand macro="input_qcov_hsp_perc" /> </expand> </inputs> <outputs> |
| b |
| diff -r 2fe07f50a41e -r c16c30e9ad5b tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Mon Dec 01 05:59:16 2014 -0500 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Sun Jul 05 10:37:27 2015 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.1.01"> +<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.1.03"> <description>Search translated nucleotide database with translated nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism> @@ -6,7 +6,7 @@ <token name="@BINARY@">tblastx</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="preamble" /> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces @@ -21,16 +21,14 @@ -db_gencode $adv_opts.db_gencode $adv_opts.strand -matrix $adv_opts.matrix -## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string -## Note -max_target_seqs overrides -num_descriptions and -num_alignments -@ADVANCED_OPTIONS@ +@ADV_FILTER_QUERY@ +@ADV_MAX_HITS@ +@ADV_WORD_SIZE@ @ADV_ID_LIST_FILTER@ +@ADV_QCOV_HSP_PERC@ ## End of advanced options: #end if </command> - - <expand macro="stdio" /> - <inputs> <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> @@ -51,6 +49,7 @@ <expand macro="input_word_size" /> <expand macro="input_parse_deflines" /> <expand macro="advanced_optional_id_files" /> + <expand macro="input_qcov_hsp_perc" /> </expand> </inputs> <outputs> |
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| diff -r 2fe07f50a41e -r c16c30e9ad5b tools/ncbi_blast_plus/repository_dependencies.xml --- a/tools/ncbi_blast_plus/repository_dependencies.xml Mon Dec 01 05:59:16 2014 -0500 +++ b/tools/ncbi_blast_plus/repository_dependencies.xml Sun Jul 05 10:37:27 2015 -0400 |
| b |
| @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="This requires the BLAST datatype definitions (e.g. the BLAST XML format)."> - <repository changeset_revision="2bda64d39931" name="blast_datatypes" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="5482a8cd0f36" name="blast_datatypes" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </repositories> |
| b |
| diff -r 2fe07f50a41e -r c16c30e9ad5b tools/ncbi_blast_plus/tool_dependencies.xml --- a/tools/ncbi_blast_plus/tool_dependencies.xml Mon Dec 01 05:59:16 2014 -0500 +++ b/tools/ncbi_blast_plus/tool_dependencies.xml Sun Jul 05 10:37:27 2015 -0400 |
| b |
| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="blast+" version="2.2.29"> - <repository changeset_revision="a2ec897aac2c" name="package_blast_plus_2_2_29" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="blast+" version="2.2.30"> + <repository changeset_revision="0fe5d5c28ea2" name="package_blast_plus_2_2_30" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |