| Previous changeset 11:4c47abb4c993 (2016-03-09) Next changeset 13:4dcc9429d6d2 (2016-12-05) |
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Commit message:
Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes. |
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modified:
test-data/rhodopsin_nucs.dbinfo.txt test-data/rhodopsin_nucs.fasta test-data/rhodopsin_nucs.fasta.nhr test-data/rhodopsin_nucs.fasta.nin test-data/rhodopsin_nucs.fasta.nog test-data/rhodopsin_nucs.fasta.nsd test-data/rhodopsin_nucs.fasta.nsi tool-data/tool_data_table_conf.xml.sample tools/ncbi_blast_plus/README.rst tools/ncbi_blast_plus/ncbi_blastdbcmd_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/tool_dependencies.xml |
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added:
test-data/rhodopsin_bufo.fasta test-data/rhodopsin_nucs.fasta.nnd test-data/rhodopsin_nucs.fasta.nni |
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| diff -r 4c47abb4c993 -r d8f2c1f560ec test-data/rhodopsin_bufo.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rhodopsin_bufo.fasta Mon Nov 07 11:29:43 2016 -0500 |
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| @@ -0,0 +1,21 @@ +>gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds +TCTTTCTAGTTTGGGGGGGGGGACTTTAAAGAGCCGCCAATATGAACGGAACAGAAGGCCCAAACTTTTACATACCCATG +TCCAACAAGACTGGGGTGGTGCGAAGCCCCTTTGAATACCCTCAGTATTACCTGGCAGAGCCATGGCAATATTCCATTCT +GTGCGCGTACATGTTCCTGCTCATTCTACTTGGGTTCCCAATCAACTTCATGACCTTGTACGTCACCATCCAGCACAAGA +AGCTCCGGACACCCTTAAACTATATCCTGCTGAATTTGGCCTTTGCCAACCACTTCATGGTCCTGTGTGGATTCACGGTG +ACAATGTACTCCTCAATGAACGGATACTTCATCCTCGGAGCCACCGGTTGCTATGTTGAAGGCTTCTTCGCTACCCTTGG +TGGTGAAATCGCCCTTTGGTCCCTGGTGGTCTTGGCCATTGAACGATACGTGGTCGTCTGTAAGCCCATGAGCAACTTCC +GATTTAGTGAGAACCATGCCGTCATGGGCGTAGCGTTCACCTGGATAATGGCTTTGTCCTGTGCTGTTCCTCCACTCCTT +GGATGGTCCAGGTACATCCCCGAGGGCATGCAGTGCTCCTGCGGAGTCGACTACTACACCCTGAAGCCCGAGGTCAACAA +CGAGTCCTTCGTCATCTACATGTTCGTCGTCCACTTCACCATCCCCCTGATTATCATTTTCTTCTGCTATGGCCGCCTGG +TGTGCACTGTGAAAGAGGCTGCAGCTCAACAGCAAGAGTCCGCCACCACCCAGAAGGCCGAGAAAGAGGTGACCAGGATG +GTGATCATCATGGTGGTCTTCTTCCTTATCTGTTGGGTCCCCTACGCCTCTGTCGCTTTCTTCATCTTCAGCAATCAGGG +CTCTGAGTTCGGCCCCATCTTCATGACCGTCCCAGCTTTCTTTGCCAAGAGTTCTTCCATCTACAACCCCGTCATCTACA +TCATGCTCAACAAGCAGTTCCGTAACTGCATGATCACCACCCTGTGCTGCGGCAAGAATCCCTTTGGAGAAGACGATGCC +TCCTCTGCCGCCACCTCCAAGACAGAGGCTTCTTCTGTTTCTTCCAGCCAGGTGTCTCCTGCATAAGACCTTCCACCAGG +CCTGTCTCAGGGTCCGCTGCCTCACACAGCTCCCACCGCCCCAACTCCGTCTCCTGCTCGCTAAGGCGGCGAAGTTCCCC +TTCCATTACATAAAACGTATCTGTTCAAGAAAGGCGACGACGAAGGAGAAGAAGAGGAGCCCCCCCGAACCCCTTCGCTG +CTGCTGAAAACGACTTGATTGCTTCTGCAACGCAACGGGGCCTTACGGCAGCGAAGGGGTTGTCATCCGGACGCGCCAAG +AATTCCTTCGAGACTGTAAATATCTTAAAGGAACCGTCCTGCTAGTTACCGACGCCGCTCCTGTAGCCGCCGTTCCCCCG +CACTCCGGCCGGTTCATACCTCTTATTTTTTTGCAATGCAACAGAAAATAATATTTTTGTTCCCACGGCTTTTCCCGGTC +AGGTCTGGTAGTGGCGGAGATTGGCCGACCCCTCGCACCTGTAATAAAGCGCAG |
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| diff -r 4c47abb4c993 -r d8f2c1f560ec test-data/rhodopsin_nucs.dbinfo.txt --- a/test-data/rhodopsin_nucs.dbinfo.txt Wed Mar 09 06:13:17 2016 -0500 +++ b/test-data/rhodopsin_nucs.dbinfo.txt Mon Nov 07 11:29:43 2016 -0500 |
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| @@ -1,7 +1,7 @@ Database: Rhodopsin nucleotides 6 sequences; 10,296 total bases -Date: Mar 8, 2016 4:58 PM Longest sequence: 4,301 bases +Date: Oct 14, 2016 2:16 PM Longest sequence: 4,301 bases Volumes: /mnt/galaxy/repositories/galaxy_blast/test-data/rhodopsin_nucs.fasta |
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| diff -r 4c47abb4c993 -r d8f2c1f560ec test-data/rhodopsin_nucs.fasta --- a/test-data/rhodopsin_nucs.fasta Wed Mar 09 06:13:17 2016 -0500 +++ b/test-data/rhodopsin_nucs.fasta Mon Nov 07 11:29:43 2016 -0500 |
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| b'@@ -1,161 +1,138 @@\n >gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA\n-ATGAACGGGACGGAGGGCCCGAACTTCTACGTGCCCTTCTCCAACAAAACGGGTGTGGTACGCAGCCCCT\n-TCGAGTACCCACAGTACTACCTGGCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTCCTGCT\n-CATCGTGCTTGGCTTCCCCATCAACTTCCTCACGCTCTACGTCACGGTCCAGCACAAGAAGCTGCGCACG\n-CCTCTCAACTACATCCTGCTCAACCTGGCCGTGGCTGACCTCTTCATGGTCTTCGGTGGCTTCACCACCA\n-CCCTCTACACCTCTCTGCATGGATACTTTGTCTTTGGGCCCACAGGATGCAATTTGGAGGGCTTCTTTGC\n-CACACTGGGCGGTGAAATTGCCCTGTGGTCTTTGGTGGTCCTGGCCATTGAGCGGTACGTGGTGGTGTGT\n-AAGCCCATGAGCAACTTCCGCTTTGGGGAGAACCATGCCATAATGGGCGTCGCTTTCACCTGGGTCATGG\n-CACTGGCCTGCGCTGCACCCCCCCTCGTTGGTTGGTCCAGGTACATCCCTGAAGGCATGCAGTGTTCATG\n-CGGGATCGACTACTACACACTCAAGCCAGAAGTCAACAACGAGTCCTTTGTCATCTACATGTTCGTGGTC\n-CACTTCACCATCCCCATGATCGTCATCTTCTTTTGCTACGGGCAGCTTGTCTTCACAGTCAAGGAGGCGG\n-CAGCCCAGCAGCAGGAGTCAGCCACCACCCAGAAGGCTGAGAAGGAGGTCACTCGCATGGTCATCATCAT\n-GGTCATTGCTTTCCTGATCTGTTGGGTGCCCTACGCCAGCGTGGCATTCTACATCTTCACCCACCAGGGG\n-TCCAACTTTGGCCCCATCTTCATGACACTCCCGGCGTTCTTCGCAAAGTCCTCCTCCATCTACAACCCTG\n-TCATCTACATCATGATGAACAAGCAGTTCCGGAACTGCATGCTCACTACCCTCTGCTGTGGCAAGAACCC\n-ACTGGGTGATGACGAGGCTTCCACAACCGGTTCCAAGACGGAGACCAGCCAGGTGGCACCGGCCTAA\n-\n+ATGAACGGGACGGAGGGCCCGAACTTCTACGTGCCCTTCTCCAACAAAACGGGTGTGGTACGCAGCCCCTTCGAGTACCC\n+ACAGTACTACCTGGCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTCCTGCTCATCGTGCTTGGCTTCCCCA\n+TCAACTTCCTCACGCTCTACGTCACGGTCCAGCACAAGAAGCTGCGCACGCCTCTCAACTACATCCTGCTCAACCTGGCC\n+GTGGCTGACCTCTTCATGGTCTTCGGTGGCTTCACCACCACCCTCTACACCTCTCTGCATGGATACTTTGTCTTTGGGCC\n+CACAGGATGCAATTTGGAGGGCTTCTTTGCCACACTGGGCGGTGAAATTGCCCTGTGGTCTTTGGTGGTCCTGGCCATTG\n+AGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTTGGGGAGAACCATGCCATAATGGGCGTCGCTTTCACC\n+TGGGTCATGGCACTGGCCTGCGCTGCACCCCCCCTCGTTGGTTGGTCCAGGTACATCCCTGAAGGCATGCAGTGTTCATG\n+CGGGATCGACTACTACACACTCAAGCCAGAAGTCAACAACGAGTCCTTTGTCATCTACATGTTCGTGGTCCACTTCACCA\n+TCCCCATGATCGTCATCTTCTTTTGCTACGGGCAGCTTGTCTTCACAGTCAAGGAGGCGGCAGCCCAGCAGCAGGAGTCA\n+GCCACCACCCAGAAGGCTGAGAAGGAGGTCACTCGCATGGTCATCATCATGGTCATTGCTTTCCTGATCTGTTGGGTGCC\n+CTACGCCAGCGTGGCATTCTACATCTTCACCCACCAGGGGTCCAACTTTGGCCCCATCTTCATGACACTCCCGGCGTTCT\n+TCGCAAAGTCCTCCTCCATCTACAACCCTGTCATCTACATCATGATGAACAAGCAGTTCCGGAACTGCATGCTCACTACC\n+CTCTGCTGTGGCAAGAACCCACTGGGTGATGACGAGGCTTCCACAACCGGTTCCAAGACGGAGACCAGCCAGGTGGCACC\n+GGCCTAA\n >gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds\n-TCTTTCTAGTTTGGGGGGGGGGACTTTAAAGAGCCGCCAATATGAACGGAACAGAAGGCCCAAACTTTTA\n-CATACCCATGTCCAACAAGACTGGGGTGGTGCGAAGCCCCTTTGAATACCCTCAGTATTACCTGGCAGAG\n-CCATGGCAATATTCCATTCTGTGCGCGTACATGTTCCTGCTCATTCTACTTGGGTTCCCAATCAACTTCA\n-TGACCTTGTACGTCACCATCCAGCACAAGAAGCTCCGGACACCCTTAAACTATATCCTGCTGAATTTGGC\n-CTTTGCCAACCACTTCATGGTCCTGTGTGGATTCACGGTGACAATGTACTCCTCAATGAACGGATACTTC\n-ATCCTCGGAGCCACCGGTTGCTATGTTGAAGGCTTCTTCGCTACCCTTGGTGGTGAAATCGCCCTTTGGT\n-CCCTGGTGGTCTTGGCCATTGAACGATACGTGGTCGTCTGTAAGCCCATGAGCAACTTCCGATTTAGTGA\n-GAACCATGCCGTCATGGGCGTAGCGTTCACCTGGATAATGGCTTTGTCCTGTGCTGTTCCTCCACTCCTT\n-GGATGGTCCAGGTACATCCCCGAGGGCATGCAGTGCTCCTGCGGAGTCGACTACTACACCCTGAAGCCCG\n-AGGTCAACAACGAGTCCTTCGTCATCTACATGTTCGTCGTCCACTTCACCATCCCCCTGATTATCATTTT\n-CTTCTGCTATGGCCGCCTGGTGTGCACTGTGAAAGAGGCTGCAGCTCAACAGCAAGAGTCCGCCACCACC\n-CAGAAGGCCGAGAAAGAGGTGACCAGGATGGTGATCATCATGGTGGTCTTCTTCCTTATCTGTTGGGTCC\n-CCTACGCCTCTGTCGCTTTCTTCATCTTCAGCAATCAGGGCTCTGAGTTCGGCCCCATCTTCATGACCGT\n-CCCAGCTTTCTTTGCCAAGAGTTCTTCCATCTACAACCCCGTCATCTACATCATGCTCAACAAGCAGTTC\n-CGTAACTGCATGATCACCACCCTGTGCTGCGGCAAGAATCCCTTTGGAGAAGACGATGCCTCCTCTGCCG\n-CCACCTCCAAGACAGAGGCTTCTTCTGTTTCTTCCAGCCAGGTGTCTCCTGCATAAGACCTTCCACCAGG\n-CCTGTCTCAGGGTCCGCTGCCTCACACAGCTCCCACCGCCCCAACTCCGTCTCCTGCTCGCTAAGGCGGC\n-GAAGTTCCCCTTCCATTACATAAAACGTATCTGTTCAAGAAAGGCGACGACGAAGGAGAAGAAGAGGAGC\n-CCCCCCGAACCCCTTCGCTGCTGCTGAAAACGACTTGATTGCTTCTGCAACGCAACGGGGCCTTACGGCA\n-GCGAAGGGGTTGTCATCCGGACGCGCCAAGAATTCCTTCGAGACTGTAAATATCTTAAAGGAACCGTCCT\n-GCTAGTTACCGACGCCGCTCCTGTAGCCGCCGTTCCCCCGCACTCCGGCCGGTTCATACCTCTTATTTTT\n-TTGCAATGCAACAGAAAATAATATTTTTGTTCCCACGGCTTTTCCCGGTCAGGTCTGGTAGTGGCGGAGA\n-TTGGCCGACCCCTCGCACCTGTAATAAAGCGCAG\n-\n+TCTTTCTAGTTTGGGGGGGGGGACTTTAAAGAGCCGCCAATATGAACGGAACAGAAGGCCC'..b'GACGAGGCCTCCACGACCGTGTCCAAGACAGAGACCAGCCAAGTGGCCCCTGCCTAA\n-\n+ATGAACGGGACCGAGGGCCCAAACTTCTACGTGCCTTTCTCCAACAAGACGGGCGTCGTACGCAGCCCCTTCGAGGCGCC\n+GCAGTACTACCTGGCTGAGCCATGGCAGTTCAGCATGCTGGCCGCCTACATGTTCCTGCTGATCATGCTTGGCTTCCCCA\n+TCAACTTCCTCACGCTGTACGTCACAGTCCAGCACAAGAAGCTGAGGACCCCCCTCAACTACATCCTGCTCAACCTGGCC\n+GTGGCAGATCTCTTCATGGTGTTCGGGGGCTTCACCACCACCCTGTATACCTCTCTGCACGGGTACTTCGTGTTCGGTCC\n+GACGGGCTGCAACCTCGAGGGCTTCTTTGCCACCTTAGGCGGTGAAATTGCACTGTGGTCCTTGGTGGTGCTAGCCATCG\n+AGCGGTACGTAGTGGTGTGCAAGCCCATGAGCAACTTCCGCTTCGGGGAGAACCACGCCATCATGGGCGTCGCATTCACC\n+TGGGTCATGGCTCTGGCCTGTGCGGCCCCCCCCCTCGTCGGCTGGTCTAGATACATCCCGGAGGGGATGCAGTGCTCGTG\n+CGGGATCGATTACTACACGCCCCACGAGGAGACCAACAATGAGTCGTTCGTCATCTACATGTTCGTTGTACACTTCATCA\n+TCCCCCTGATTGTCATATTCTTCTGCTACGGGCAGCTGGTCTTCACCGTCAAGGAGGCTGCAGCCCAGCAGCAGGAGTCG\n+GCCACCACTCAGAAGGCCGAGAAGGAGGTCACGCGTATGGTCATCATCATGGTCATCGCTTTCCTCATATGCTGGCTGCC\n+CTACGCAGGTGTGGCGTTCTACATCTTCACCCATCAGGGATCCGACTTTGGCCCCATCTTCATGACCATCCCGGCTTTCT\n+TTGCCAAGACGTCTGCCGTCTATAACCCCGTCATCTACATCATGATGAACAAGCAGTTCCGGAACTGCATGGTCACCACT\n+CTCTGCTGTGGCAAGAACCCCCTAGGTGACGACGAGGCCTCCACGACCGTGTCCAAGACAGAGACCAGCCAAGTGGCCCC\n+TGCCTAA\n >gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds\n-CCGCTACTGACGAACCGCAACCATGAACGGCACTGAGGGACCTAACTTCTACATCCCCATGTCAAACGCC\n-ACTGGTGTAGTGAGGAGTCCATTTGAATACCCGCAGTACTACCTTGCAGAACCATGGGCTTTCTCAGCTC\n-TGTCTGCCTACATGTTCTTCCTGATTATCGCCGGATTCCCCATCAACTTCCTCACCCTGTATGTCACCAT\n-CGAACATAAGAAACTGAGGACCCCACTGAACTACATTCTGCTGAACCTGGCCGTGGCCGACCTCTTCATG\n-GTGTTTGGCGGATTCACCACCACGATGTACACCTCCATGCACGGCTACTTTGTCTTCGGCCCCACCGGCT\n-GCAACATCGAAGGGTTCTTCGCCACCCTCGGCGGCGAGATTGCCCTCTGGTGCCTCGTTGTCCTGGCCAT\n-TGAAAGGTGGATGGTCGTCTGCAAGCCAGTGACCAATTTCCGCTTCGGTGAGAGCCATGCCATCATGGGT\n-GTCATGGTGACCTGGACCATGGCATTGGCCTGTGCCCTCCCCCCTCTCTTCGGCTGGTCTCGGTACATTC\n-CGGAAGGTCTGCAGTGCTCGTGCGGGATCGACTACTATACCCGGGCGCCTGGGATCAACAATGAGTCCTT\n-TGTGATCTACATGTTTACCTGCCACTTCTCCATCCCACTCGCCGTCATCTCTTTCTGCTACGGCCGACTG\n-GTGTGCACCGTCAAAGAGGCCGCTGCCCAGCAACAGGAGTCCGAGACCACCCAGAGGGCTGAGCGGGAGG\n-TCACCCGCATGGTCGTCATCATGGTCATCTCCTTCCTGGTCTGCTGGGTGCCCTATGCCAGTGTGGCCTG\n-GTACATCTTTACCCACCAGGGAAGCACTTTTGGGCCCATCTTCATGACCATTCCATCCTTCTTTGCCAAG\n-AGTTCAGCCCTCTACAACCCCATGATCTACATCTGCATGAACAAGCAGTTCCGCCATTGCATGATCACCA\n-CCCTCTGCTGTGGGAAGAACCCCTTCGAGGAGGAGGATGGAGCGTCCGCCACTAGCTCTAAAACTGAGGC\n-TTCATCCGTGTCCTCCAGCTCTGTCTCCCCGGCATAAACCTTGTTTGACCGAACACCACGCATCAACACA\n-AAGACCAAGAATGCTGACTAAATGCTAACATTTCAGGGAAATCCAAAGACTTTTTACTATTTTTTTACAC\n-AACCATATAGGTTGCAAACAGAGGTTTAGCCCTGTTTACAGGTTGTCATCAATGTGATGTCAGTATGTAC\n-AATATAGTCAACTTGATAGCAAGTTGTTGGCTTATTTCAGATTGTATGGGCAATGTAATCAACCATATGT\n-GAAATAAATTGCAA\n+CCGCTACTGACGAACCGCAACCATGAACGGCACTGAGGGACCTAACTTCTACATCCCCATGTCAAACGCCACTGGTGTAG\n+TGAGGAGTCCATTTGAATACCCGCAGTACTACCTTGCAGAACCATGGGCTTTCTCAGCTCTGTCTGCCTACATGTTCTTC\n+CTGATTATCGCCGGATTCCCCATCAACTTCCTCACCCTGTATGTCACCATCGAACATAAGAAACTGAGGACCCCACTGAA\n+CTACATTCTGCTGAACCTGGCCGTGGCCGACCTCTTCATGGTGTTTGGCGGATTCACCACCACGATGTACACCTCCATGC\n+ACGGCTACTTTGTCTTCGGCCCCACCGGCTGCAACATCGAAGGGTTCTTCGCCACCCTCGGCGGCGAGATTGCCCTCTGG\n+TGCCTCGTTGTCCTGGCCATTGAAAGGTGGATGGTCGTCTGCAAGCCAGTGACCAATTTCCGCTTCGGTGAGAGCCATGC\n+CATCATGGGTGTCATGGTGACCTGGACCATGGCATTGGCCTGTGCCCTCCCCCCTCTCTTCGGCTGGTCTCGGTACATTC\n+CGGAAGGTCTGCAGTGCTCGTGCGGGATCGACTACTATACCCGGGCGCCTGGGATCAACAATGAGTCCTTTGTGATCTAC\n+ATGTTTACCTGCCACTTCTCCATCCCACTCGCCGTCATCTCTTTCTGCTACGGCCGACTGGTGTGCACCGTCAAAGAGGC\n+CGCTGCCCAGCAACAGGAGTCCGAGACCACCCAGAGGGCTGAGCGGGAGGTCACCCGCATGGTCGTCATCATGGTCATCT\n+CCTTCCTGGTCTGCTGGGTGCCCTATGCCAGTGTGGCCTGGTACATCTTTACCCACCAGGGAAGCACTTTTGGGCCCATC\n+TTCATGACCATTCCATCCTTCTTTGCCAAGAGTTCAGCCCTCTACAACCCCATGATCTACATCTGCATGAACAAGCAGTT\n+CCGCCATTGCATGATCACCACCCTCTGCTGTGGGAAGAACCCCTTCGAGGAGGAGGATGGAGCGTCCGCCACTAGCTCTA\n+AAACTGAGGCTTCATCCGTGTCCTCCAGCTCTGTCTCCCCGGCATAAACCTTGTTTGACCGAACACCACGCATCAACACA\n+AAGACCAAGAATGCTGACTAAATGCTAACATTTCAGGGAAATCCAAAGACTTTTTACTATTTTTTTACACAACCATATAG\n+GTTGCAAACAGAGGTTTAGCCCTGTTTACAGGTTGTCATCAATGTGATGTCAGTATGTACAATATAGTCAACTTGATAGC\n+AAGTTGTTGGCTTATTTCAGATTGTATGGGCAATGTAATCAACCATATGTGAAATAAATTGCAA\n' 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| diff -r 4c47abb4c993 -r d8f2c1f560ec test-data/rhodopsin_nucs.fasta.nhr |
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| Binary file test-data/rhodopsin_nucs.fasta.nhr has changed |
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| diff -r 4c47abb4c993 -r d8f2c1f560ec test-data/rhodopsin_nucs.fasta.nin |
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| Binary file test-data/rhodopsin_nucs.fasta.nin has changed |
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| diff -r 4c47abb4c993 -r d8f2c1f560ec test-data/rhodopsin_nucs.fasta.nnd |
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| Binary file test-data/rhodopsin_nucs.fasta.nnd has changed |
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| diff -r 4c47abb4c993 -r d8f2c1f560ec test-data/rhodopsin_nucs.fasta.nni |
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| Binary file test-data/rhodopsin_nucs.fasta.nni has changed |
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| diff -r 4c47abb4c993 -r d8f2c1f560ec test-data/rhodopsin_nucs.fasta.nog |
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| Binary file test-data/rhodopsin_nucs.fasta.nog has changed |
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| diff -r 4c47abb4c993 -r d8f2c1f560ec test-data/rhodopsin_nucs.fasta.nsd --- a/test-data/rhodopsin_nucs.fasta.nsd Wed Mar 09 06:13:17 2016 -0500 +++ b/test-data/rhodopsin_nucs.fasta.nsd Mon Nov 07 11:29:43 2016 -0500 |
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| @@ -1,6 +1,13 @@ -gnl|bl_ord_id|00 -gnl|bl_ord_id|11 -gnl|bl_ord_id|22 -gnl|bl_ord_id|33 -gnl|bl_ord_id|44 -gnl|bl_ord_id|55 +ab0438175 +ab043817.15 +ab0624174 +ab062417.14 +bbu599211 +gq2903032 +gq290303.12 +gq2903123 +gq290312.13 +nm_0010092420 +nm_001009242.10 +u599211 +u59921.11 |
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| diff -r 4c47abb4c993 -r d8f2c1f560ec test-data/rhodopsin_nucs.fasta.nsi |
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| Binary file test-data/rhodopsin_nucs.fasta.nsi has changed |
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| diff -r 4c47abb4c993 -r d8f2c1f560ec tool-data/tool_data_table_conf.xml.sample --- a/tool-data/tool_data_table_conf.xml.sample Wed Mar 09 06:13:17 2016 -0500 +++ b/tool-data/tool_data_table_conf.xml.sample Mon Nov 07 11:29:43 2016 -0500 |
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| @@ -1,13 +1,13 @@ <tables> - <table name="blastdb" comment_char="#"> + <table name="blastdb" comment_char="#" allow_duplicate_entries="False"> <columns>value, name, path</columns> <file path="tool-data/blastdb.loc" /> </table> - <table name="blastdb_p" comment_char="#"> + <table name="blastdb_p" comment_char="#" allow_duplicate_entries="False"> <columns>value, name, path</columns> <file path="tool-data/blastdb_p.loc" /> </table> - <table name="blastdb_d" comment_char="#"> + <table name="blastdb_d" comment_char="#" allow_duplicate_entries="False"> <columns>value, name, path</columns> <file path="tool-data/blastdb_d.loc" /> </table> |
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| diff -r 4c47abb4c993 -r d8f2c1f560ec tools/ncbi_blast_plus/README.rst --- a/tools/ncbi_blast_plus/README.rst Wed Mar 09 06:13:17 2016 -0500 +++ b/tools/ncbi_blast_plus/README.rst Mon Nov 07 11:29:43 2016 -0500 |
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| @@ -118,8 +118,9 @@ four cores to each BLAST job. In addition, the BLAST+ wrappers also support high level parallelism by task -splitting if ``use_tasked_jobs = True`` is enabled in your ``universe_wsgi.ini`` -configuration file. Essentially, the FASTA input query files are broken up into +splitting if ``use_tasked_jobs = True`` is enabled in the ``config/galaxy.ini`` +configuration file (previously ``universe_wsgi.ini`` on older versions of +Galaxy). Essentially, the FASTA input query files are broken up into batches of 1000 sequences, a separate BLAST child job is run for each chunk, and then the BLAST output files are merged (in order). This is transparent for the end user. @@ -229,7 +230,10 @@ (contribution from Bjoern Gruening and Daniel Blankenberg). v0.1.08 - Allow searching against multiple locally installed databases (contribution from Gildas Le Corguillé and Emma Prudent). - - Minor Python style changes (internal change only). + - Minor XML and Python style changes (internal change only). + - Set ``allow_duplicate_entries="False"`` in sample configuration file + ``tool_data_table_conf.xml``. + - Fix identifers with pipes in ``blastdbcmd`` wrapper (Devon Ryan). ======= ====================================================================== |
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| diff -r 4c47abb4c993 -r d8f2c1f560ec tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Wed Mar 09 06:13:17 2016 -0500 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Mon Nov 07 11:29:43 2016 -0500 |
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| @@ -16,8 +16,8 @@ -entry_batch "$id_opts.entries" #else: ##Perform some simple search/replaces to remove whitespace -##and make it comma separated, and escape any pipe characters --entry "$id_opts.entries.replace('\r',',').replace('\n',',').replace(' ','').replace(',,',',').replace(',,',',').strip(',').replace('|','\|')" +##and make it comma separated. Quoted so don't escape pipes. +-entry "$id_opts.entries.replace('\r',',').replace('\n',',').replace(' ','').replace(',,',',').replace(',,',',').strip(',')" #end if ##When building a BLAST database, to ensure unique IDs makeblastdb will @@ -78,6 +78,30 @@ <param name="outfmt" value="original" /> <output name="seq" file="four_human_proteins.fasta" ftype="fasta" /> </test> + <test> + <param name="db_opts|db_type" value="nucl" /> + <param name="db_opts|database" value="rhodopsin_nucs" /> + <param name="id_opts|id_type" value="prompt" /> + <param name="id_opts|entries" value="all" /> + <param name="outfmt" value="original" /> + <output name="seq" file="rhodopsin_nucs.fasta" ftype="fasta" /> + </test> + <test> + <param name="db_opts|db_type" value="nucl" /> + <param name="db_opts|database" value="rhodopsin_nucs" /> + <param name="id_opts|id_type" value="prompt" /> + <param name="id_opts|entries" value="U59921.1" /> + <param name="outfmt" value="original" /> + <output name="seq" file="rhodopsin_bufo.fasta" ftype="fasta" /> + </test> + <test> + <param name="db_opts|db_type" value="nucl" /> + <param name="db_opts|database" value="rhodopsin_nucs" /> + <param name="id_opts|id_type" value="prompt" /> + <param name="id_opts|entries" value="gi|2734705|gb|U59921.1|BBU59921" /> + <param name="outfmt" value="original" /> + <output name="seq" file="rhodopsin_bufo.fasta" ftype="fasta" /> + </test> </tests> <help> |
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| diff -r 4c47abb4c993 -r d8f2c1f560ec tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml Wed Mar 09 06:13:17 2016 -0500 +++ b/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml Mon Nov 07 11:29:43 2016 -0500 |
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| @@ -74,7 +74,7 @@ More information about segmasker can be found in the `BLAST Command Line Applications User Manual`_. -.. _BLAST Command Line Applications User Manual: http://www.ncbi.nlm.nih.gov/books/NBK1763/ +.. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/ **References** |
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| diff -r 4c47abb4c993 -r d8f2c1f560ec tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Wed Mar 09 06:13:17 2016 -0500 +++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Mon Nov 07 11:29:43 2016 -0500 |
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| @@ -85,7 +85,7 @@ More information about dustmasker can be found in the `BLAST Command Line Applications User Manual`_. -.. _BLAST Command Line Applications User Manual: http://www.ncbi.nlm.nih.gov/books/NBK1763/ +.. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/ .. _DUST: http://www.ncbi.nlm.nih.gov/pubmed/16796549 **References** |
| b |
| diff -r 4c47abb4c993 -r d8f2c1f560ec tools/ncbi_blast_plus/ncbi_macros.xml --- a/tools/ncbi_blast_plus/ncbi_macros.xml Wed Mar 09 06:13:17 2016 -0500 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Mon Nov 07 11:29:43 2016 -0500 |
| b |
| @@ -133,7 +133,7 @@ <xml name="input_query_gencode"> <param name="query_gencode" type="select" label="Query genetic code"> <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> - <option value="1" select="True">1. Standard</option> + <option value="1" selected="True">1. Standard</option> <option value="2">2. Vertebrate Mitochondrial</option> <option value="3">3. Yeast Mitochondrial</option> <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> @@ -156,7 +156,7 @@ <xml name="input_db_gencode"> <param name="db_gencode" type="select" label="Database/subject genetic code"> <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> - <option value="1" select="True">1. Standard</option> + <option value="1" selected="True">1. Standard</option> <option value="2">2. Vertebrate Mitochondrial</option> <option value="3">3. Yeast Mitochondrial</option> <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> @@ -296,7 +296,7 @@ </param> </xml> <xml name="input_qcov_hsp_perc"> - <param name="qcov_hsp_perc" type="float" value="0" min="0" max="100" label="Minimum query coverage per hsp (percentage, 0 to 100)" help="See also the output column qhspcov"/> + <param name="qcov_hsp_perc" type="float" value="0" min="0" max="100" label="Minimum query coverage per hsp (percentage, 0 to 100)" help="See also the output column qcovhsp"/> </xml> <xml name="advanced_options"> <conditional name="adv_opts"> |
| b |
| diff -r 4c47abb4c993 -r d8f2c1f560ec tools/ncbi_blast_plus/ncbi_makeblastdb.xml --- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Wed Mar 09 06:13:17 2016 -0500 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Mon Nov 07 11:29:43 2016 -0500 |
| b |
| @@ -190,7 +190,7 @@ **Documentation** -http://www.ncbi.nlm.nih.gov/books/NBK1763/ +https://www.ncbi.nlm.nih.gov/books/NBK279690/ **References** |
| b |
| diff -r 4c47abb4c993 -r d8f2c1f560ec tools/ncbi_blast_plus/ncbi_makeprofiledb.xml --- a/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Wed Mar 09 06:13:17 2016 -0500 +++ b/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Mon Nov 07 11:29:43 2016 -0500 |
| b |
| @@ -113,7 +113,7 @@ More information about makeprofiledb can be found in the `BLAST Command Line Applications User Manual`_. -.. _BLAST Command Line Applications User Manual: http://www.ncbi.nlm.nih.gov/books/NBK1763/ +.. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/ **References** |
| b |
| diff -r 4c47abb4c993 -r d8f2c1f560ec tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Wed Mar 09 06:13:17 2016 -0500 +++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Mon Nov 07 11:29:43 2016 -0500 |
| b |
| @@ -77,14 +77,14 @@ *Kog* - PSSMs from automatically aligned sequences and sequence fragments classified in the KOGs resource, the eukaryotic -counterpart to COGs, see http://www.ncbi.nlm.nih.gov/COG/new/ +counterpart to COGs, see http://www.ncbi.nlm.nih.gov/COG/ *Cog* - PSSMs from automatically aligned sequences and sequence fragments classified in the COGs resource, which focuses primarily -on prokaryotes, see http://www.ncbi.nlm.nih.gov/COG/new/ +on prokaryotes, see http://www.ncbi.nlm.nih.gov/COG/ *Pfam* - PSSMs from Pfam-A seed alignment database, see -http://pfam.sanger.ac.uk/ +http://xfam.org/ *Smart* - PSSMs from SMART domain alignment database, see http://smart.embl-heidelberg.de/ |
| b |
| diff -r 4c47abb4c993 -r d8f2c1f560ec tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Wed Mar 09 06:13:17 2016 -0500 +++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Mon Nov 07 11:29:43 2016 -0500 |
| b |
| @@ -77,14 +77,14 @@ *Kog* - PSSMs from automatically aligned sequences and sequence fragments classified in the KOGs resource, the eukaryotic -counterpart to COGs, see http://www.ncbi.nlm.nih.gov/COG/new/ +counterpart to COGs, see http://www.ncbi.nlm.nih.gov/COG/ *Cog* - PSSMs from automatically aligned sequences and sequence fragments classified in the COGs resource, which focuses primarily -on prokaryotes, see http://www.ncbi.nlm.nih.gov/COG/new/ +on prokaryotes, see http://www.ncbi.nlm.nih.gov/COG/ *Pfam* - PSSMs from Pfam-A seed alignment database, see -http://pfam.sanger.ac.uk/ +http://xfam.org/ *Smart* - PSSMs from SMART domain alignment database, see http://smart.embl-heidelberg.de/ |
| b |
| diff -r 4c47abb4c993 -r d8f2c1f560ec tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml Wed Mar 09 06:13:17 2016 -0500 +++ b/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml Mon Nov 07 11:29:43 2016 -0500 |
| b |
| @@ -87,7 +87,7 @@ More information about segmasker can be found in the `BLAST Command Line Applications User Manual`_. -.. _BLAST Command Line Applications User Manual: http://www.ncbi.nlm.nih.gov/books/NBK1763/ +.. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/ .. _SEG: http://www.ncbi.nlm.nih.gov/pubmed/8743706 **References** |
| b |
| diff -r 4c47abb4c993 -r d8f2c1f560ec tools/ncbi_blast_plus/tool_dependencies.xml --- a/tools/ncbi_blast_plus/tool_dependencies.xml Wed Mar 09 06:13:17 2016 -0500 +++ b/tools/ncbi_blast_plus/tool_dependencies.xml Mon Nov 07 11:29:43 2016 -0500 |
| b |
| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="blast+" version="2.2.31"> - <repository changeset_revision="4df9cdbc6e61" name="package_blast_plus_2_2_31" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="6e4a0aaa3357" name="package_blast_plus_2_2_31" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |