| Previous changeset 58:cc1ab05a5588 (2022-12-19) |
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Commit message:
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit eb397ba9bd3d2f3db13757f3bce094a89c4de9b3 |
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modified:
test-data/blastn_chimera_vs_three_human_max1.txt 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/cd00003_and_cd00008.pin test-data/four_human_proteins.fasta.pin test-data/four_human_proteins_taxid.fasta.pin test-data/rhodopsin_nucs.fasta.nin test-data/tblastn_four_human_vs_rhodopsin.html test-data/tblastn_four_human_vs_rhodopsin.tabular test-data/tblastn_four_human_vs_rhodopsin.xml test-data/tblastn_four_human_vs_rhodopsin_deflines.tabular test-data/tblastn_four_human_vs_rhodopsin_ext.tabular test-data/three_human_mRNA.fasta.gz test-data/three_human_mRNA.fasta.nin test-data/tool_data_table_conf.xml.test tool-data/tool_data_table_conf.xml.sample tools/ncbi_blast_plus/README.rst tools/ncbi_blast_plus/blastxml_to_tabular.xml tools/ncbi_blast_plus/get_species_taxids.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 |
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added:
tool-data/all_fasta.loc.sample |
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| diff -r cc1ab05a5588 -r 491dc0cd6a0d test-data/blastn_chimera_vs_three_human_max1.txt --- a/test-data/blastn_chimera_vs_three_human_max1.txt Mon Dec 19 09:36:39 2022 +0000 +++ b/test-data/blastn_chimera_vs_three_human_max1.txt Wed Mar 26 16:42:53 2025 +0000 |
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| @@ -1,4 +1,4 @@ -BLASTN 2.10.1+ +BLASTN 2.16.0+ Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb @@ -346,7 +346,7 @@ Database: Just 3 human mRNA sequences - Posted date: Sep 9, 2020 11:23 PM + Posted date: Sep 22, 2023 4:36 PM Number of letters in database: 10,732 Number of sequences in database: 3 |
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| diff -r cc1ab05a5588 -r 491dc0cd6a0d test-data/blastn_rhodopsin_vs_three_human.xml --- a/test-data/blastn_rhodopsin_vs_three_human.xml Mon Dec 19 09:36:39 2022 +0000 +++ b/test-data/blastn_rhodopsin_vs_three_human.xml Wed Mar 26 16:42:53 2025 +0000 |
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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 2.10.1+</BlastOutput_version> + <BlastOutput_version>BLASTN 2.16.0+</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 cc1ab05a5588 -r 491dc0cd6a0d test-data/blastp_four_human_vs_rhodopsin.xml --- a/test-data/blastp_four_human_vs_rhodopsin.xml Mon Dec 19 09:36:39 2022 +0000 +++ b/test-data/blastp_four_human_vs_rhodopsin.xml Wed Mar 26 16:42:53 2025 +0000 |
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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 2.10.1+</BlastOutput_version> + <BlastOutput_version>BLASTP 2.16.0+</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>Q9BS26</BlastOutput_query-ID> |
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| diff -r cc1ab05a5588 -r 491dc0cd6a0d test-data/blastx_rhodopsin_vs_four_human.xml --- a/test-data/blastx_rhodopsin_vs_four_human.xml Mon Dec 19 09:36:39 2022 +0000 +++ b/test-data/blastx_rhodopsin_vs_four_human.xml Wed Mar 26 16:42:53 2025 +0000 |
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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 2.10.1+</BlastOutput_version> + <BlastOutput_version>BLASTX 2.16.0+</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 cc1ab05a5588 -r 491dc0cd6a0d test-data/cd00003_and_cd00008.pin |
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| Binary file test-data/cd00003_and_cd00008.pin has changed |
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| diff -r cc1ab05a5588 -r 491dc0cd6a0d test-data/four_human_proteins.fasta.pin |
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| Binary file test-data/four_human_proteins.fasta.pin has changed |
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| diff -r cc1ab05a5588 -r 491dc0cd6a0d test-data/four_human_proteins_taxid.fasta.pin |
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| Binary file test-data/four_human_proteins_taxid.fasta.pin has changed |
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| diff -r cc1ab05a5588 -r 491dc0cd6a0d 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 cc1ab05a5588 -r 491dc0cd6a0d test-data/tblastn_four_human_vs_rhodopsin.html --- a/test-data/tblastn_four_human_vs_rhodopsin.html Mon Dec 19 09:36:39 2022 +0000 +++ b/test-data/tblastn_four_human_vs_rhodopsin.html Wed Mar 26 16:42:53 2025 +0000 |
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| @@ -3,7 +3,7 @@ <BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099"> <PRE> -<b>TBLASTN 2.10.1+</b> +<b>TBLASTN 2.14.1+</b> <b><a @@ -89,7 +89,7 @@ gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA <a href=#Subject_1>732</a> 0.0 gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene f... <a href=#Subject_5>711</a> 0.0 -gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodops... <a href=#Subject_4>658</a> 0.0 +gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodops... <a href=#Subject_4>682</a> 0.0 gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complet... <a href=#Subject_2>646</a> 0.0 gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh ... <a href=#Subject_6>626</a> 0.0 gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 2002043... <a href=#Subject_3>229</a> 3e-67 @@ -165,7 +165,7 @@ (RHO) mRNA, partial cds Length=983 - Score = 658 bits (1517), Expect = 0.0, Method: Compositional matrix adjust. + Score = 682 bits (1573), Expect = 0.0, Method: Compositional matrix adjust. Identities = 310/326 (95%), Positives = 322/326 (99%), Gaps = 0/326 (0%) Frame = +1 |
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| diff -r cc1ab05a5588 -r 491dc0cd6a0d test-data/tblastn_four_human_vs_rhodopsin.tabular --- a/test-data/tblastn_four_human_vs_rhodopsin.tabular Mon Dec 19 09:36:39 2022 +0000 +++ b/test-data/tblastn_four_human_vs_rhodopsin.tabular Wed Mar 26 16:42:53 2025 +0000 |
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| @@ -1,6 +1,6 @@ sp|P08100|OPSD_HUMAN gi|57163782|ref|NM_001009242.1| 96.552 348 12 0 1 348 1 1044 0.0 732 sp|P08100|OPSD_HUMAN gi|18148870|dbj|AB062417.1| 93.391 348 23 0 1 348 1 1044 0.0 711 -sp|P08100|OPSD_HUMAN gi|283855822|gb|GQ290312.1| 95.092 326 16 0 11 336 1 978 0.0 658 +sp|P08100|OPSD_HUMAN gi|283855822|gb|GQ290312.1| 95.092 326 16 0 11 336 1 978 0.0 682 sp|P08100|OPSD_HUMAN gi|2734705|gb|U59921.1|BBU59921 84.795 342 51 1 1 341 42 1067 0.0 646 sp|P08100|OPSD_HUMAN gi|12583664|dbj|AB043817.1| 82.164 342 60 1 1 341 23 1048 0.0 626 sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.243 74 5 0 239 312 3147 3368 1.34e-71 151 |
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| diff -r cc1ab05a5588 -r 491dc0cd6a0d test-data/tblastn_four_human_vs_rhodopsin.xml --- a/test-data/tblastn_four_human_vs_rhodopsin.xml Mon Dec 19 09:36:39 2022 +0000 +++ b/test-data/tblastn_four_human_vs_rhodopsin.xml Wed Mar 26 16:42:53 2025 +0000 |
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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 2.10.1+</BlastOutput_version> + <BlastOutput_version>TBLASTN 2.16.0+</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> @@ -149,8 +149,8 @@ <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> - <Hsp_bit-score>658.198</Hsp_bit-score> - <Hsp_score>1517</Hsp_score> + <Hsp_bit-score>682.354</Hsp_bit-score> + <Hsp_score>1573</Hsp_score> <Hsp_evalue>0</Hsp_evalue> <Hsp_query-from>11</Hsp_query-from> <Hsp_query-to>336</Hsp_query-to> |
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| diff -r cc1ab05a5588 -r 491dc0cd6a0d test-data/tblastn_four_human_vs_rhodopsin_deflines.tabular --- a/test-data/tblastn_four_human_vs_rhodopsin_deflines.tabular Mon Dec 19 09:36:39 2022 +0000 +++ b/test-data/tblastn_four_human_vs_rhodopsin_deflines.tabular Wed Mar 26 16:42:53 2025 +0000 |
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| @@ -1,6 +1,6 @@ P08100 NM_001009242.1 96.552 348 12 0 1 348 1 1044 0.0 732 P08100 AB062417.1 93.391 348 23 0 1 348 1 1044 0.0 711 -P08100 GQ290312.1 95.092 326 16 0 11 336 1 978 0.0 658 +P08100 GQ290312.1 95.092 326 16 0 11 336 1 978 0.0 682 P08100 U59921.1 84.795 342 51 1 1 341 42 1067 0.0 646 P08100 AB043817.1 82.164 342 60 1 1 341 23 1048 0.0 626 P08100 GQ290303.1 93.243 74 5 0 239 312 3147 3368 1.34e-71 151 |
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| diff -r cc1ab05a5588 -r 491dc0cd6a0d test-data/tblastn_four_human_vs_rhodopsin_ext.tabular --- a/test-data/tblastn_four_human_vs_rhodopsin_ext.tabular Mon Dec 19 09:36:39 2022 +0000 +++ b/test-data/tblastn_four_human_vs_rhodopsin_ext.tabular Wed Mar 26 16:42:53 2025 +0000 |
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| @@ -1,6 +1,6 @@ sp|P08100|OPSD_HUMAN gi|57163782|ref|NM_001009242.1| 96.552 348 12 0 1 348 1 1044 0.0 732 gi|57163782|ref|NM_001009242.1| 1689 336 343 0 98.56 0 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA 348 1047 N/A sp|P08100|OPSD_HUMAN gi|18148870|dbj|AB062417.1| 93.391 348 23 0 1 348 1 1044 0.0 711 gi|18148870|dbj|AB062417.1| 1640 325 337 0 96.84 0 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348 1047 N/A -sp|P08100|OPSD_HUMAN gi|283855822|gb|GQ290312.1| 95.092 326 16 0 11 336 1 978 0.0 658 gi|283855822|gb|GQ290312.1| 1517 310 322 0 98.77 0 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT 348 983 N/A +sp|P08100|OPSD_HUMAN gi|283855822|gb|GQ290312.1| 95.092 326 16 0 11 336 1 978 0.0 682 gi|283855822|gb|GQ290312.1| 1573 310 322 0 98.77 0 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT 348 983 N/A sp|P08100|OPSD_HUMAN gi|2734705|gb|U59921.1|BBU59921 84.795 342 51 1 1 341 42 1067 0.0 646 gi|2734705|gb|U59921.1|BBU59921 1489 290 320 1 93.57 0 3 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE 348 1574 N/A sp|P08100|OPSD_HUMAN gi|12583664|dbj|AB043817.1| 82.164 342 60 1 1 341 23 1048 0.0 626 gi|12583664|dbj|AB043817.1| 1444 281 311 1 90.94 0 2 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE 348 1344 N/A sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.243 74 5 0 239 312 3147 3368 1.34e-71 151 gi|283855845|gb|GQ290303.1| 342 69 73 0 98.65 0 3 ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ ESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ 348 4301 N/A |
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| diff -r cc1ab05a5588 -r 491dc0cd6a0d test-data/three_human_mRNA.fasta.gz |
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| Binary file test-data/three_human_mRNA.fasta.gz has changed |
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| diff -r cc1ab05a5588 -r 491dc0cd6a0d test-data/three_human_mRNA.fasta.nin |
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| diff -r cc1ab05a5588 -r 491dc0cd6a0d test-data/tool_data_table_conf.xml.test --- a/test-data/tool_data_table_conf.xml.test Mon Dec 19 09:36:39 2022 +0000 +++ b/test-data/tool_data_table_conf.xml.test Wed Mar 26 16:42:53 2025 +0000 |
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| @@ -12,4 +12,8 @@ <columns>value, name, path</columns> <file path="${__HERE__}/blastdb_d.loc" /> </table> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/all_fasta.loc" /> + </table> </tables> |
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| diff -r cc1ab05a5588 -r 491dc0cd6a0d tool-data/all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Wed Mar 26 16:42:53 2025 +0000 |
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| @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# |
| b |
| diff -r cc1ab05a5588 -r 491dc0cd6a0d tool-data/tool_data_table_conf.xml.sample --- a/tool-data/tool_data_table_conf.xml.sample Mon Dec 19 09:36:39 2022 +0000 +++ b/tool-data/tool_data_table_conf.xml.sample Wed Mar 26 16:42:53 2025 +0000 |
| b |
| @@ -11,4 +11,8 @@ <columns>value, name, path</columns> <file path="tool-data/blastdb_d.loc" /> </table> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc.sample" /> + </table> </tables> |
| b |
| diff -r cc1ab05a5588 -r 491dc0cd6a0d tools/ncbi_blast_plus/README.rst --- a/tools/ncbi_blast_plus/README.rst Mon Dec 19 09:36:39 2022 +0000 +++ b/tools/ncbi_blast_plus/README.rst Wed Mar 26 16:42:53 2025 +0000 |
| b |
| @@ -136,6 +136,11 @@ ============== =============================================================== Version Changes -------------- --------------------------------------------------------------- +2.14.1+galaxy2 - Add usage of genome FASTA files on the Galaxy server with + ``makeblastdb`` (contribution from Wolfgang Maier and + Elischa Berger) +2.14.1+galaxy1 - Fix for get_species_taxids +2.14.1+galaxy0 - Updated for NCBI BLAST+ 2.14.1 release. 2.10.1+galaxy3 - Silenced ``deltablast`` warning about using ``-num_threads`` with ``--subject`` (i.e. FASTA file from your history). 2.10.1+galaxy2 - Fixed ``dc-megablast`` option in ``ncbi_blastn_wrapper.xml`` |
| b |
| diff -r cc1ab05a5588 -r 491dc0cd6a0d tools/ncbi_blast_plus/blastxml_to_tabular.xml --- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml Mon Dec 19 09:36:39 2022 +0000 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml Wed Mar 26 16:42:53 2025 +0000 |
| [ |
| @@ -7,7 +7,7 @@ <requirement type="package" version="3.9">python</requirement> </requirements> <version_command>python $__tool_directory__/blastxml_to_tabular.py --version</version_command> - <command detect_errors="aggressive"> + <command detect_errors="aggressive"><![CDATA[ python $__tool_directory__/blastxml_to_tabular.py -o '$tabular_file' #if $output.out_format == "cols": #set cols = (str($output.std_cols)+","+str($output.ext_cols)).replace("None", " ").replace(",,", ",").replace(",", " ") @@ -16,7 +16,7 @@ -c '$output.out_format' #end if #for i in $blastxml_file#'${i}' #end for# - </command> + ]]></command> <inputs> <param name="blastxml_file" type="data" format="blastxml" multiple="true" label="BLAST results as XML"/> <conditional name="output"> @@ -66,73 +66,97 @@ <tests> <test> <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> - <param name="out_format" value="std" /> + <conditional name="output"> + <param name="out_format" value="std" /> + </conditional> <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin.tabluar --> <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted.tabular" ftype="tabular" /> </test> <test> <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> - <param name="out_format" value="ext" /> + <conditional name="output"> + <param name="out_format" value="ext" /> + </conditional> <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin_22c.tabluar --> <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted_ext.tabular" ftype="tabular" /> </test> <test> <param name="blastxml_file" value="blastp_sample.xml" ftype="blastxml" /> - <param name="out_format" value="std" /> + <conditional name="output"> + <param name="out_format" value="std" /> + </conditional> <!-- Note this has some white space differences from the actual blastp output --> <output name="tabular_file" file="blastp_sample_converted.tabular" ftype="tabular" /> </test> <test> <param name="blastxml_file" value="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" /> - <param name="out_format" value="std" /> + <conditional name="output"> + <param name="out_format" value="std" /> + </conditional> <!-- Note this has some white space differences from the actual blastx output --> <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted.tabular" ftype="tabular" /> </test> <test> <param name="blastxml_file" value="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" /> - <param name="out_format" value="ext" /> + <conditional name="output"> + <param name="out_format" value="ext" /> + </conditional> <!-- Note this has some white space and XXXX masking differences from the actual blastx output --> <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted_ext.tabular" ftype="tabular" /> </test> <test> <param name="blastxml_file" value="blastx_sample.xml" ftype="blastxml" /> - <param name="out_format" value="std" /> + <conditional name="output"> + <param name="out_format" value="std" /> + </conditional> <!-- Note this has some white space differences from the actual blastx output --> <output name="tabular_file" file="blastx_sample_converted.tabular" ftype="tabular" /> </test> <test> <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" /> - <param name="out_format" value="std" /> + <conditional name="output"> + <param name="out_format" value="std" /> + </conditional> <!-- Note this has some white space differences from the actual blastp output --> <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_std.tabular" ftype="tabular" /> </test> <test> <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" /> - <param name="out_format" value="ext" /> + <conditional name="output"> + <param name="out_format" value="ext" /> + </conditional> <!-- Note this has some white space differences from the actual blastp output --> <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_ext.tabular" ftype="tabular" /> </test> <test> <param name="blastxml_file" value="blastn_arabidopsis.xml" ftype="blastxml" /> - <param name="out_format" value="std" /> + <conditional name="output"> + <param name="out_format" value="std" /> + </conditional> <output name="tabular_file" file="blastn_arabidopsis.standard.tabular" ftype="tabular" /> </test> <test> <param name="blastxml_file" value="blastn_arabidopsis.xml" ftype="blastxml" /> - <param name="out_format" value="ext" /> + <conditional name="output"> + <param name="out_format" value="ext" /> + </conditional> <output name="tabular_file" file="blastn_arabidopsis.extended.tabular" ftype="tabular" /> </test> <!-- there are some harmless white space differences in our conversion to the BLAST+ output here: --> <test> <param name="blastxml_file" value="blastn_rhodopsin_vs_three_human.xml" ftype="blastxml" /> - <param name="out_format" value="std" /> + <conditional name="output"> + <param name="out_format" value="std" /> + </conditional> <output name="tabular_file" file="blastn_rhodopsin_vs_three_human_converted.tabular" ftype="tabular" /> </test> <test> <param name="blastxml_file" value="blastn_rhodopsin_vs_three_human.xml" ftype="blastxml" /> - <param name="out_format" value="cols" /> - <param name="std_cols" value="qseqid,sseqid,pident" /> - <param name="ext_cols" value="qlen,slen" /> + <conditional name="output"> + <param name="out_format" value="cols" /> + <param name="std_cols" value="qseqid,sseqid,pident" /> + <param name="ext_cols" value="qlen,slen" /> + </conditional> <output name="tabular_file" file="blastn_rhodopsin_vs_three_human.columns.tabular" ftype="tabular" /> </test> </tests> |
| b |
| diff -r cc1ab05a5588 -r 491dc0cd6a0d tools/ncbi_blast_plus/get_species_taxids.xml --- a/tools/ncbi_blast_plus/get_species_taxids.xml Mon Dec 19 09:36:39 2022 +0000 +++ b/tools/ncbi_blast_plus/get_species_taxids.xml Wed Mar 26 16:42:53 2025 +0000 |
| [ |
| @@ -3,21 +3,22 @@ <macros> <import>ncbi_macros.xml</import> </macros> - <expand macro="preamble"/> + <expand macro="requirements"/> + <version_command>echo "@TOOL_VERSION@"</version_command> <command detect_errors="aggressive"><![CDATA[ #if $type_cond.type_sel == 'names' #for name in $type_cond.names.split(',') - taxid=\$(get_species_taxids.sh -n '$name' | grep Taxid | sed 's/Taxid://') && - if [ -z \$taxid ]; then + taxid=\$(get_species_taxids.sh -n '$name' | grep Taxid | sed 's/Taxid\s*:\s*//') && + if [ -z "\$taxid" ]; then >&2 echo "could not find taxid for $name" && exit 1; else echo " $name -> \$taxid"; fi && - get_species_taxids.sh -t \$taxid >> species_ids.txt && + get_species_taxids.sh -t "\$taxid" >> species_ids.txt && #end for #else #for taxid in $type_cond.ids.split(',') - get_species_taxids.sh -t $taxid >> species_ids.txt && + get_species_taxids.sh -t "$taxid" >> species_ids.txt && #end for #end if sort -n -u species_ids.txt > '$output' @@ -93,14 +94,6 @@ Returns a list of species taxids for a taxon. It relies on the get_species_taxids.sh script of the BLAST+ package https://www.ncbi.nlm.nih.gov/books/NBK546209/ -------- - -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations"/> </tool> |
| b |
| diff -r cc1ab05a5588 -r 491dc0cd6a0d tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Mon Dec 19 09:36:39 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Wed Mar 26 16:42:53 2025 +0000 |
| [ |
| @@ -5,11 +5,11 @@ <import>ncbi_macros.xml</import> </macros> <expand macro="preamble" /> - <command detect_errors="aggressive"> + <command detect_errors="aggressive"><![CDATA[ blastdbcmd @DBCMD_OPTS@ -info -out "$info" - </command> + ]]></command> <inputs> <expand macro="input_conditional_choose_db_type" /> </inputs> @@ -46,14 +46,6 @@ switch to give summary information about a BLAST database, such as the size (number of sequences and total length) and date. -------- - -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations" /> </tool> |
| b |
| diff -r cc1ab05a5588 -r 491dc0cd6a0d tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Mon Dec 19 09:36:39 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Wed Mar 26 16:42:53 2025 +0000 |
| [ |
| @@ -5,14 +5,12 @@ <import>ncbi_macros.xml</import> </macros> <expand macro="preamble" /> - <command detect_errors="aggressive" strict="true"> + <command detect_errors="aggressive" strict="true"><![CDATA[ ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces blastdbcmd @DBCMD_OPTS@ -##TODO: What about -ctrl_a and -target_only as advanced options? - #if $id_opts.id_type=="file": -entry_batch '$id_opts.entries' #else: @@ -43,11 +41,11 @@ #if str($outfmt)=="blastid": -out '$seq' #else if sys.platform == "darwin": -| sed -E 's/^>(lcl\||gnl\|BL_ORD_ID\|[0-9]* )/>/1' > "$seq" +| sed -E 's/^>(lcl\||gnl\|BL_ORD_ID\|[0-9]* )/>/1' > "$seq" #else: -| sed 's/>\(lcl|\|gnl|BL_ORD_ID|[0-9]* \)/>/1' > "$seq" +| sed 's/>\(lcl|\|gnl|BL_ORD_ID|[0-9]* \)/>/1' > "$seq" #end if - </command> + ]]></command> <inputs> <expand macro="input_conditional_choose_db_type" /> <conditional name="id_opts"> @@ -66,6 +64,7 @@ <option value="original">FASTA with original identifiers</option> <option value="blastid">FASTA with BLAST assigned identifiers</option> </param> + <!-- TODO: What about -ctrl_a and -target_only as advanced options? --> </inputs> <outputs> @@ -153,14 +152,6 @@ @CLI_OPTIONS@ -------- - -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations" /> </tool> |
| b |
| diff -r cc1ab05a5588 -r 491dc0cd6a0d tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Mon Dec 19 09:36:39 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Wed Mar 26 16:42:53 2025 +0000 |
| [ |
| b'@@ -4,10 +4,8 @@\n <token name="@BINARY@">blastn</token>\n <import>ncbi_macros.xml</import>\n </macros>\n- <expand macro="parallelism" />\n <expand macro="preamble" />\n- <command detect_errors="aggressive">\n-<![CDATA[\n+ <command detect_errors="aggressive"><![CDATA[\n ## The command is a Cheetah template which allows some Python based syntax.\n ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces\n blastn\n@@ -36,8 +34,7 @@\n @ADV_GAPEXTEND@\n ## End of advanced options:\n #end if\n-]]>\n- </command>\n+ ]]></command>\n <inputs>\n <expand macro="nucl_query" />\n <expand macro="input_conditional_nucleotide_db" />\n@@ -83,93 +80,147 @@\n <tests>\n <test>\n <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />\n- <param name="db_opts_selector" value="file" />\n- <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" />\n- <param name="database" value="" />\n+ <conditional name="db_opts">\n+ <param name="db_opts_selector" value="file" />\n+ <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" />\n+ <param name="database" value="" />\n+ </conditional>\n <param name="evalue_cutoff" value="1e-40" />\n- <param name="out_format" value="5" />\n- <param name="adv_opts_selector" value="basic" />\n+ <conditional name="output">\n+ <param name="out_format" value="5" />\n+ </conditional>\n+ <conditional name="adv_opts">\n+ <param name="adv_opts_selector" value="basic" />\n+ </conditional>\n <output name="output1" file="blastn_rhodopsin_vs_three_human.xml" ftype="blastxml" />\n </test>\n <test>\n <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />\n- <param name="db_opts_selector" value="file" />\n- <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" />\n- <param name="database" value="" />\n+ <conditional name="db_opts">\n+ <param name="db_opts_selector" value="file" />\n+ <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" />\n+ <param name="database" value="" />\n+ </conditional>\n <param name="evalue_cutoff" value="1e-40" />\n- <param name="out_format" value="6" />\n- <param name="adv_opts_selector" value="basic" />\n+ <conditional name="output">\n+ <param name="out_format" value="6" />\n+ </conditional>\n+ <conditional name="adv_opts">\n+ <param name="adv_opts_selector" value="basic" />\n+ </conditional>\n <output name="output1" file="blastn_rhodopsin_vs_three_human.tabular" ftype="tabular" />\n </test>\n <test>\n <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />\n- <param name="db_opts_selector" value="file" />\n- <param name="subject" value="three_human_mRNA.fasta.gz" ftype="fasta.gz" />\n- <param name="database" value="" />\n+ <conditional name="db_opts">\n+ <param name="db_opts_selector" value="file" />\n+ <param name="subject" value="three_human_mRNA.fasta.gz" ftype="fasta.gz" />\n+ <param name="database" value="" />\n+ </conditional>\n <param name="evalue_cutoff" value="1e-40" />\n- <param name="out_format" value="6" />\n- <param name="adv_opts_selector" value="basic" />\n+ <conditional name="output">\n+ <param name="out_format" value="6" />\n+ </conditional>\n+ <conditional name="adv_opts">\n+ <param name="adv_opts_selector" value="basic" />\n+ </conditional>\n <output name="output1" file="blastn_rhodopsin_'..b'="database" value="three_human_mRNA" />\n+ </conditional>\n+ <conditional name="output">\n+ <param name="out_format" value="0" />\n+ </conditional>\n+ <conditional name="adv_opts">\n+ <param name="adv_opts_selector" value="advanced" />\n+ <param name="max_hits" value="1" />\n+ </conditional>\n <output name="output1" file="blastn_chimera_vs_three_human_max1.txt" ftype="txt" />\n </test>\n <test>\n <param name="query" value="chimera.fasta" ftype="fasta" />\n- <param name="db_opts_selector" value="db" />\n- <param name="database" value="three_human_mRNA" />\n- <param name="out_format" value="6" />\n+ <conditional name="db_opts">\n+ <param name="db_opts_selector" value="db" />\n+ <param name="database" value="three_human_mRNA" />\n+ </conditional>\n+ <conditional name="output">\n+ <param name="out_format" value="6" />\n+ </conditional>\n <output name="output1" file="blastn_chimera_vs_three_human_db.tabular" ftype="tabular" />\n </test>\n <test>\n <param name="query" value="chimera.fasta" ftype="fasta" />\n- <param name="db_opts_selector" value="db" />\n- <param name="database" value="rhodopsin_nucs" />\n- <param name="out_format" value="6" />\n+ <conditional name="db_opts">\n+ <param name="db_opts_selector" value="db" />\n+ <param name="database" value="rhodopsin_nucs" />\n+ </conditional>\n+ <conditional name="output">\n+ <param name="out_format" value="6" />\n+ </conditional>\n <output name="output1" file="blastn_chimera_vs_rhodopsin_db.tabular" ftype="tabular" />\n </test>\n <test>\n <param name="query" value="chimera.fasta" ftype="fasta" />\n- <param name="db_opts_selector" value="db" />\n- <param name="database" value="rhodopsin_nucs" />\n- <param name="out_format" value="6" />\n- <param name="adv_opts_selector" value="advanced" />\n- <param name="max_hsps" value="1" />\n+ <conditional name="db_opts">\n+ <param name="db_opts_selector" value="db" />\n+ <param name="database" value="rhodopsin_nucs" />\n+ </conditional>\n+ <conditional name="output">\n+ <param name="out_format" value="6" />\n+ </conditional>\n+ <conditional name="adv_opts">\n+ <param name="adv_opts_selector" value="advanced" />\n+ <param name="max_hsps" value="1" />\n+ </conditional>\n <output name="output1" file="blastn_chimera_vs_rhodopsin_db_max_hsps1.tabular" ftype="tabular" />\n </test>\n <!-- next test is passing in two blast databases -->\n <test>\n <param name="query" value="chimera.fasta" ftype="fasta" />\n- <param name="db_opts_selector" value="db" />\n- <param name="database" value="three_human_mRNA,rhodopsin_nucs" />\n- <param name="out_format" value="6" />\n+ <conditional name="db_opts">\n+ <param name="db_opts_selector" value="db" />\n+ <param name="database" value="three_human_mRNA,rhodopsin_nucs" />\n+ </conditional>\n+ <conditional name="output">\n+ <param name="out_format" value="6" />\n+ </conditional>\n <output name="output1" file="blastn_chimera_vs_three_human_and_rhodopsin_db.tabular" ftype="tabular" />\n </test>\n </tests>\n@@ -193,14 +244,6 @@\n \n @CLI_OPTIONS@\n \n--------\n-\n-**References**\n-\n-If you use this Galaxy tool in work leading to a scientific publication please\n-cite the following papers:\n-\n-@REFERENCES@\n </help>\n <expand macro="blast_citations" />\n </tool>\n' |
| b |
| diff -r cc1ab05a5588 -r 491dc0cd6a0d tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Mon Dec 19 09:36:39 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Wed Mar 26 16:42:53 2025 +0000 |
| [ |
| b'@@ -4,9 +4,8 @@\n <token name="@BINARY@">blastp</token>\n <import>ncbi_macros.xml</import>\n </macros>\n- <expand macro="parallelism" />\n <expand macro="preamble" />\n- <command detect_errors="aggressive">\n+ <command detect_errors="aggressive"><![CDATA[\n ## The command is a Cheetah template which allows some Python based syntax.\n ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces\n blastp\n@@ -31,7 +30,7 @@\n @ADV_COMP_BASED_STATS@\n ## End of advanced options:\n #end if\n- </command>\n+ ]]></command>\n <inputs>\n <expand macro="prot_query" />\n \n@@ -75,92 +74,136 @@\n <tests>\n <test>\n <param name="query" value="four_human_proteins.fasta" ftype="fasta" />\n- <param name="db_opts_selector" value="file" />\n- <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />\n- <param name="database" value="" />\n+ <conditional name="db_opts">\n+ <param name="db_opts_selector" value="file" />\n+ <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />\n+ <param name="database" value="" />\n+ </conditional>\n <param name="evalue_cutoff" value="1e-8" />\n <param name="blast_type" value="blastp" />\n- <param name="out_format" value="5" />\n- <param name="adv_opts_selector" value="advanced" />\n- <param name="filter_query" value="false" />\n- <param name="matrix" value="BLOSUM62" />\n- <param name="max_hits" value="0" />\n- <param name="word_size" value="" />\n- <param name="window_size" value="40" />\n- <param name="parse_deflines" value="true" />\n- <param name="qcov_hsp_perc" value="25" />\n+ <conditional name="output">\n+ <param name="out_format" value="5" />\n+ </conditional>\n+ <conditional name="adv_opts">\n+ <param name="adv_opts_selector" value="advanced" />\n+ <param name="filter_query" value="false" />\n+ <conditional name="matrix_gapcosts">\n+ <param name="matrix" value="BLOSUM62" />\n+ </conditional>\n+ <param name="max_hits" value="0" />\n+ <!-- <param name="word_size" value="" /> -->\n+ <param name="window_size" value="40" />\n+ <param name="parse_deflines" value="true" />\n+ <param name="qcov_hsp_perc" value="25" />\n+ </conditional>\n <output name="output1" file="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />\n </test>\n <test>\n <param name="query" value="four_human_proteins.fasta" ftype="fasta" />\n- <param name="db_opts_selector" value="file" />\n- <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />\n- <param name="database" value="" />\n+ <conditional name="db_opts">\n+ <param name="db_opts_selector" value="file" />\n+ <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />\n+ <param name="database" value="" />\n+ </conditional>\n <param name="evalue_cutoff" value="1e-8" />\n <param name="blast_type" value="blastp" />\n- <param name="out_format" value="6" />\n- <param name="adv_opts_selector" value="advanced" />\n- <param name="filter_query" value="false" />\n- <param name="matrix" value="BLOSUM62" />\n- <param name="max_hits" value="0" />\n- <param name="word_size" value="" />\n- <param name="window_size" value="40" />\n- <param name="parse_deflines" value="true" />\n- <param name="qcov_hsp_perc" value="25" />\n+ <conditional name="output">\n+ <param name="out_format" value="6" />\n+ </conditi'..b'/>\n+ <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />\n+ <param name="database" value="" />\n+ </conditional>\n <param name="evalue_cutoff" value="1e-8" />\n <param name="blast_type" value="blastp" />\n- <param name="out_format" value="6" />\n- <param name="adv_opts_selector" value="basic" />\n+ <conditional name="output">\n+ <param name="out_format" value="6" />\n+ </conditional>\n+ <conditional name="adv_opts">\n+ <param name="adv_opts_selector" value="basic" />\n+ </conditional>\n <output name="output1" file="blastp_rhodopsin_vs_four_human.tabular" ftype="tabular" />\n </test>\n <test>\n <param name="query" value="rhodopsin_peptides.fasta" ftype="fasta" />\n- <param name="db_opts_selector" value="file" />\n- <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />\n- <param name="database" value="" />\n+ <conditional name="db_opts">\n+ <param name="db_opts_selector" value="file" />\n+ <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />\n+ <param name="database" value="" />\n+ </conditional>\n <param name="evalue_cutoff" value="200000" />\n <param name="blast_type" value="blastp-short" />\n- <param name="out_format" value="6" />\n- <param name="adv_opts_selector" value="basic" />\n+ <conditional name="output">\n+ <param name="out_format" value="6" />\n+ </conditional>\n+ <conditional name="adv_opts">\n+ <param name="adv_opts_selector" value="basic" />\n+ </conditional>\n <output name="output1" file="blastp_rhodopsin_peptides_vs_four_human.tabular" ftype="tabular" />\n </test>\n <test>\n <param name="query" value="rhodopsin_proteins.fasta" ftype="fasta" />\n- <param name="db_opts_selector" value="file" />\n- <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />\n- <param name="database" value="" />\n+ <conditional name="db_opts">\n+ <param name="db_opts_selector" value="file" />\n+ <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />\n+ <param name="database" value="" />\n+ </conditional>\n <param name="evalue_cutoff" value="1e-8"/>\n <param name="blast_type" value="blastp" />\n- <param name="out_format" value="6"/>\n- <param name="adv_opts_selector" value="advanced"/>\n- <param name="window_size" value="35" />\n- <param name="matrix" value="BLOSUM62" />\n- <param name="gap_costs" value="-gapopen 11 -gapextend 1"/>\n- <param name="comp_based_stats" value="3" />\n+ <conditional name="output">\n+ <param name="out_format" value="6"/>\n+ </conditional>\n+ <conditional name="adv_opts">\n+ <param name="adv_opts_selector" value="advanced"/>\n+ <param name="window_size" value="35" />\n+ <conditional name="matrix_gapcosts">\n+ <param name="matrix" value="BLOSUM62" />\n+ <param name="gap_costs" value="-gapopen 11 -gapextend 1"/>\n+ </conditional>\n+ <param name="comp_based_stats" value="3" />\n+ </conditional>\n <output name="output1" file="blastp_rhodopsin_adv_vs_four_human.tabular" ftype="tabular" />\n </test>\n </tests>\n@@ -183,14 +226,6 @@\n \n @CLI_OPTIONS@\n \n--------\n-\n-**References**\n-\n-If you use this Galaxy tool in work leading to a scientific publication please\n-cite the following papers:\n-\n-@REFERENCES@\n </help>\n <expand macro="blast_citations" />\n </tool>\n' |
| b |
| diff -r cc1ab05a5588 -r 491dc0cd6a0d tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Mon Dec 19 09:36:39 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Wed Mar 26 16:42:53 2025 +0000 |
| [ |
| @@ -4,9 +4,8 @@ <token name="@BINARY@">blastx</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="parallelism" /> <expand macro="preamble" /> - <command detect_errors="aggressive"> + <command detect_errors="aggressive"><![CDATA[ ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces blastx @@ -31,7 +30,7 @@ @ADV_COMP_BASED_STATS@ ## End of advanced options: #end if - </command> + ]]></command> <inputs> <expand macro="nucl_query" /> @@ -68,58 +67,90 @@ <tests> <test> <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="database" value="" /> + </conditional> <param name="evalue_cutoff" value="1e-10" /> - <param name="out_format" value="5" /> - <param name="adv_opts_selector" value="basic" /> + <conditional name="output"> + <param name="out_format" value="5" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="basic" /> + </conditional> <output name="output1" file="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" /> </test> <test> <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="database" value="" /> + </conditional> <param name="evalue_cutoff" value="1e-10" /> - <param name="out_format" value="6" /> - <param name="adv_opts_selector" value="basic" /> + <conditional name="output"> + <param name="out_format" value="6" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="basic" /> + </conditional> <output name="output1" file="blastx_rhodopsin_vs_four_human.tabular" ftype="tabular" /> </test> <test> <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="database" value="" /> + </conditional> <param name="evalue_cutoff" value="1e-10" /> - <param name="out_format" value="ext" /> - <param name="adv_opts_selector" value="basic" /> + <conditional name="output"> + <param name="out_format" value="ext" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="basic" /> + </conditional> <output name="output1" file="blastx_rhodopsin_vs_four_human_ext.tabular" ftype="tabular" /> </test> <test> <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="database" value="" /> + </conditional> <param name="evalue_cutoff" value="1e-10" /> - <param name="out_format" value="cols" /> - <param name="std_cols" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore" /> - <param name="ext_cols" value="sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles" /> - <param name="ids_cols" value="qgi,qacc,qaccver,sallseqid,sgi,sallgi,sacc,saccver,sallacc,stitle" /> - <param name="misc_cols" value="sstrand,frames,btop,qcovs,qcovhsp" /> - <param name="tax_cols" value="staxids,sscinames,scomnames,sblastnames,sskingdoms" /> - <param name="adv_opts_selector" value="basic" /> + <conditional name="output"> + <param name="out_format" value="cols" /> + <param name="std_cols" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore" /> + <param name="ext_cols" value="sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles" /> + <param name="ids_cols" value="qgi,qacc,qaccver,sallseqid,sgi,sallgi,sacc,saccver,sallacc,stitle" /> + <param name="misc_cols" value="sstrand,frames,btop,qcovs,qcovhsp" /> + <param name="tax_cols" value="staxids,sscinames,scomnames,sblastnames,sskingdoms" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="basic" /> + </conditional> <output name="output1" file="blastx_rhodopsin_vs_four_human_all.tabular" ftype="tabular" /> </test> <test> <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="database" value="" /> + </conditional> <param name="evalue_cutoff" value="1e-10" /> - <param name="out_format" value="6" /> - <param name="adv_opts_selector" value="advanced" /> - <param name="matrix" value="BLOSUM62" /> + <conditional name="output"> + <param name="out_format" value="6" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="advanced" /> + <conditional name="matrix_gapcosts"> + <param name="matrix" value="BLOSUM62" /> + </conditional> + </conditional> <output name="output1" file="blastx_rhodopsin_adv_vs_four_human.tabular" ftype="tabular" /> </test> </tests> @@ -142,14 +173,6 @@ @CLI_OPTIONS@ -------- - -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations" /> </tool> |
| b |
| diff -r cc1ab05a5588 -r 491dc0cd6a0d tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml Mon Dec 19 09:36:39 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml Wed Mar 26 16:42:53 2025 +0000 |
| [ |
| @@ -5,7 +5,7 @@ <import>ncbi_macros.xml</import> </macros> <expand macro="preamble" /> - <command detect_errors="aggressive"> + <command detect_errors="aggressive"><![CDATA[ ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces convert2blastmask @@ -15,7 +15,7 @@ $parse_seqids -out '$outfile' -outfmt $outformat - </command> + ]]></command> <inputs> <param name="infile" argument="-in" type="data" format="fasta" label="Masked FASTA file"/> <param argument="-masking_algorithm" type="select" label="Used masking algorithm"> @@ -76,12 +76,6 @@ .. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/ -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations" /> </tool> |
| b |
| diff -r cc1ab05a5588 -r 491dc0cd6a0d tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Mon Dec 19 09:36:39 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Wed Mar 26 16:42:53 2025 +0000 |
| [ |
| @@ -6,7 +6,7 @@ <import>ncbi_macros.xml</import> </macros> <expand macro="preamble" /> - <command detect_errors="aggressive"> + <command detect_errors="aggressive"><![CDATA[ ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces dustmasker @@ -14,12 +14,18 @@ -in '${db_opts.database.fields.path}' -infmt blastdb #elif $db_opts.db_opts_selector == "histdb": -in '${os.path.join($db_opts.histdb.files_path, "blastdb")}' -infmt blastdb -#else: - -in '$subject' -infmt fasta +#else + -in + #if $subject.ext == "fasta" + '$subject' + #else + <(gunzip -c '$subject') + #end if + -infmt fasta #end if -out '$outfile' -window $window -level $level -linker $linker -outfmt $outformat - </command> + ]]></command> <inputs> <expand macro="input_conditional_nucleotide_db" /> <param argument="-window" type="integer" value="64" label="DUST window length" /> @@ -49,8 +55,10 @@ </outputs> <tests> <test> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> + </conditional> <param name="window" value="64" /> <param name="level" value="20" /> <param name="linker" value="1" /> @@ -58,8 +66,10 @@ <output name="outfile" file="dustmasker_three_human.fasta" /> </test> <test> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="three_human_mRNA.fasta.gz" ftype="fasta.gz" /> + </conditional> <param name="window" value="64" /> <param name="level" value="20" /> <param name="linker" value="1" /> @@ -67,8 +77,10 @@ <output name="outfile" file="dustmasker_three_human.maskinfo-asn1-binary" /> </test> <test> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> + </conditional> <param name="window" value="64" /> <param name="level" value="20" /> <param name="linker" value="1" /> @@ -88,12 +100,6 @@ .. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/ .. _DUST: https://www.ncbi.nlm.nih.gov/pubmed/16796549 -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations" /> </tool> |
| b |
| diff -r cc1ab05a5588 -r 491dc0cd6a0d tools/ncbi_blast_plus/ncbi_macros.xml --- a/tools/ncbi_blast_plus/ncbi_macros.xml Mon Dec 19 09:36:39 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Wed Mar 26 16:42:53 2025 +0000 |
| [ |
| @@ -1,18 +1,24 @@ <macros> - <token name="@TOOL_VERSION@">2.10.1</token> - <token name="@VERSION_SUFFIX@">3</token> - <token name="@PROFILE@">16.10</token> - <xml name="parallelism"> - <!-- 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" /> + <token name="@TOOL_VERSION@">2.16.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">22.01</token> + + <xrefs> + <xref type="bio.tools">blast</xref> + </xrefs> + + <xml name="preamble"> + <expand macro="requirements"> + <yield/> + </expand> + <version_command>@BINARY@ -version</version_command> </xml> - <xml name="preamble"> + <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">blast</requirement> <yield /> </requirements> - <version_command>@BINARY@ -version</version_command> </xml> <xml name="nucl_query"> @@ -655,7 +661,7 @@ -outfmt '6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen salltitles' #elif str($output.out_format)=="cols" ##Pick your own columns. Galaxy gives us it comma separated, BLAST+ wants space separated: -##TODO - Can we catch the user picking no columns and raise an error here? +##Can we catch the user picking no columns and raise an error here? #set cols = (str($output.std_cols)+","+str($output.ext_cols)+","+str($output.ids_cols)+","+str($output.misc_cols)+","+str($output.tax_cols)).replace("None", "").replace(",,", ",").replace(",", " ").strip() -outfmt '6 $cols' #else: @@ -769,19 +775,6 @@ #end if ]]></token> - <token name="@REFERENCES@"><![CDATA[ -Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo (2015). -NCBI BLAST+ integrated into Galaxy. *GigaScience* 4:39 -https://doi.org/10.1186/s13742-015-0080-7 - -Christiam Camacho et al. (2009). -BLAST+: architecture and applications. -*BMC Bioinformatics* 15;10:421. -https://doi.org/10.1186/1471-2105-10-421 - -This wrapper is available to install into other Galaxy Instances via the Galaxy -Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus - ]]></token> <xml name="blast_citations"> <citations> <citation type="doi">10.1093/nar/25.17.3389</citation> |
| b |
| diff -r cc1ab05a5588 -r 491dc0cd6a0d tools/ncbi_blast_plus/ncbi_makeblastdb.xml --- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Mon Dec 19 09:36:39 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Wed Mar 26 16:42:53 2025 +0000 |
| [ |
| b'@@ -8,21 +8,36 @@\n <requirement type="package" version="3.9">python</requirement>\n </expand>\n <command detect_errors="aggressive" strict="true"><![CDATA[\n+#set $inputs = []\n+#set $input_compression = []\n+#for r in $input.selection:\n+ #if $input.type == "protein":\n+ #silent $inputs.append($r.input_file)\n+ #silent $input_compression.append($r.input_file.is_of_type(\'fasta.gz\'))\n+ #elif $r.nuc_choice.source == "history":\n+ #silent $inputs.append($r.nuc_choice.input_file)\n+ #silent $input_compression.append($r.nuc_choice.input_file.is_of_type(\'fasta.gz\'))\n+ #else:\n+ #silent $inputs.append($r.nuc_choice.input_file.fields.path)\n+ #silent $input_compression.append(False)\n+ #end if\n+#end for\n+\n python $__tool_directory__/check_no_duplicates.py\n ##First check for duplicates (since BLAST+ 2.2.28 fails to do so)\n ##and abort (via the ampersand ampersand trick) if any are found.\n-#for i in $input_file#\'${i}\' #end for#\n+#for i in $inputs#\'$i\' #end for#\n &&\n ##makeblastdb does not like input redirects of the sort\n ##makeblastdb -in <(gunzip -c gzipped_fasta_file)\n ##therefore we\'re cramming everything\n ##into a single cat command below\n cat\n-#for i in $input_file:\n- #if $i.is_of_type(\'fasta.gz\') and $i.ext != "fasta":\n- <(gunzip -c ${i})\n+#for i, is_gzipped in zip($inputs, $input_compression):\n+ #if $is_gzipped:\n+ <(gunzip -c \'$i\')\n #else:\n- ${i}\n+ \'$i\'\n #end if\n #end for\n | makeblastdb -out \'${os.path.join($outfile.files_path, "blastdb")}\'\n@@ -36,7 +51,12 @@\n ##Would default to being based on the cryptic Galaxy filenames, which is unhelpful\n -title \'BLAST Database\'\n #end if\n--dbtype $dbtype\n+-dbtype\n+#if $input.type == "protein":\n+ prot\n+#else:\n+ nucl\n+#end if\n ## --------------------------------------------------------------------\n ## Masking\n ## --------------------------------------------------------------------\n@@ -52,7 +72,6 @@\n ## --------------------------------------------------------------------\n #if $tax.taxselect == \'id\':\n -taxid $tax.taxid\n-## TODO - Can we use a tabular file for the taxonomy mapping?\n ## #else if $tax.taxselect == \'map\':\n ## -taxid_map $tax.taxmap\n #end if\n@@ -61,15 +80,39 @@\n > \'$outfile\'\n ]]></command>\n <inputs>\n- <param argument="-dbtype" type="select" display="radio" label="Molecule type of input">\n- <option value="prot">protein</option>\n- <option value="nucl">nucleotide</option>\n- </param>\n- <!-- TODO Allow merging of existing BLAST databases (conditional on the database type)?\n- NOTE Double check the new database would be self contained first\n- -->\n- <!-- Note this is a mandatory parameter - default should be most recent FASTA file -->\n- <param name="input_file" argument="-in" type="data" multiple="true" optional="false" format="fasta,fasta.gz" label="Input FASTA files(s)" help="One or more FASTA files" />\n+ <conditional name="input">\n+ <param argument="-dbtype" name="type" type="select" label="Molecule type of input">\n+ <option value="protein">protein</option>\n+ <option value="nucleotide">nucleotide</option>\n+ </param>\n+ <!-- TODO Allow merging of existing BLAST databases (conditional on the database type)?\n+ NOTE Double check the new database would be self contained first\n+ -->\n+ <when value="protein">\n+ <repeat name="selection" title="Select input" min="1" default="1">\n+ <!-- Note this is a mandatory parameter - default should be most recent FASTA file -->\n+ <param name="input_file" argument="-in" type="data" format="fasta,fasta.gz" label="FASTA input" help="FASTA file with one or more sequences to add to the database" />\n+ </repeat>\n+ </when>\n+ <when value="nucleotide">\n+ <repeat name="selecti'..b'e_seqids" value="" />\n+ <param name="parse_seqids" value="false" />\n <param name="hash_index" value="true" />\n <param name="mask_data_file" value="segmasker_four_human.maskinfo-asn1" ftype="maskinfo-asn1" />\n <output name="outfile" compare="contains" file="four_human_proteins.fasta.log.txt" ftype="blastdbp">\n@@ -169,13 +228,50 @@\n </output>\n </test>\n <test>\n- <param name="dbtype" value="nucl" />\n- <param name="input_file" value="three_human_mRNA.fasta.gz" ftype="fasta.gz" />\n+ <conditional name="input">\n+ <param name="type" value="nucleotide"/>\n+ <repeat name="selection">\n+ <conditional name="nuc_choice">\n+ <param name="source" value="history"/>\n+ <param name="input_file" value="three_human_mRNA.fasta.gz" ftype="fasta.gz" />\n+ </conditional> \n+ </repeat>\n+ </conditional> \n <param name="title" value="Just 3 human mRNA sequences" />\n- <param name="parse_seqids" value="" />\n+ <param name="parse_seqids" value="false" />\n <param name="hash_index" value="true" />\n- <param name="taxselect" value="id" />\n- <param name="taxid" value="9606" />\n+ <conditional name="tax">\n+ <param name="taxselect" value="id" />\n+ <param name="taxid" value="9606" />\n+ </conditional>\n+ <output name="outfile" compare="contains" file="three_human_mRNA.fasta.log.txt" ftype="blastdbn">\n+ <extra_files type="file" value="three_human_mRNA.fasta.nhr" name="blastdb.nhr" />\n+ <extra_files type="file" value="three_human_mRNA.fasta.nin" name="blastdb.nin" compare="sim_size" delta="8" />\n+ <extra_files type="file" value="three_human_mRNA.fasta.nsq" name="blastdb.nsq" />\n+ <extra_files type="file" value="three_human_mRNA.fasta.nog" name="blastdb.nog" />\n+ <extra_files type="file" value="three_human_mRNA.fasta.nhd" name="blastdb.nhd" />\n+ <extra_files type="file" value="three_human_mRNA.fasta.nhi" name="blastdb.nhi" />\n+ <extra_files type="file" value="three_human_mRNA.fasta.nsd" name="blastdb.nsd" />\n+ <extra_files type="file" value="three_human_mRNA.fasta.nsi" name="blastdb.nsi" />\n+ </output>\n+ </test>\n+ <test>\n+ <conditional name="input">\n+ <param name="type" value="nucleotide"/>\n+ <repeat name="selection">\n+ <conditional name="nuc_choice">\n+ <param name="source" value="cached"/>\n+ <param name="input_file" value="three_human_mRNA" />\n+ </conditional> \n+ </repeat>\n+ </conditional> \n+ <param name="title" value="Just 3 human mRNA sequences" />\n+ <param name="parse_seqids" value="false" />\n+ <param name="hash_index" value="true" />\n+ <conditional name="tax">\n+ <param name="taxselect" value="id" />\n+ <param name="taxid" value="9606" />\n+ </conditional>\n <output name="outfile" compare="contains" file="three_human_mRNA.fasta.log.txt" ftype="blastdbn">\n <extra_files type="file" value="three_human_mRNA.fasta.nhr" name="blastdb.nhr" />\n <extra_files type="file" value="three_human_mRNA.fasta.nin" name="blastdb.nin" compare="sim_size" delta="8" />\n@@ -206,12 +302,6 @@\n For this reason, it\'s best to apply all masks at once to minimize the number of unnecessary intermediate databases.\n -->\n \n-**References**\n-\n-If you use this Galaxy tool in work leading to a scientific publication please\n-cite the following papers:\n-\n-@REFERENCES@\n </help>\n <expand macro="blast_citations" />\n </tool>\n' |
| b |
| diff -r cc1ab05a5588 -r 491dc0cd6a0d tools/ncbi_blast_plus/ncbi_makeprofiledb.xml --- a/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Mon Dec 19 09:36:39 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Wed Mar 26 16:42:53 2025 +0000 |
| [ |
| @@ -5,9 +5,9 @@ <import>ncbi_macros.xml</import> </macros> <expand macro="preamble" /> - <command detect_errors="aggressive" strict="true"> + <command detect_errors="aggressive" strict="true"><![CDATA[ ##Unlike makeblastdb, makeprofiledb needs directory to exist already: -mkdir -p $outfile.files_path && +mkdir -p $outfile.files_path && makeprofiledb -blastdb_version 4 -out '${os.path.join($outfile.files_path, "blastdb")}' @@ -35,13 +35,13 @@ -exclude_invalid $exclude_invalid -logfile '$outfile' - </command> + ]]></command> <configfiles> - <configfile name="infiles"> + <configfile name="infiles"><![CDATA[ #for $infile in $input_file ${infile} #end for - </configfile> + ]]></configfile> </configfiles> <inputs> <param name="input_file" argument="-in" type="data" multiple="true" optional="false" format="pssm-asn1" @@ -89,7 +89,9 @@ <test> <param name="input_file" value="cd00003.smp,cd00008.smp" ftype="pssm-asn1" /> <param name="title" value="Just 2 PSSM matrices" /> - <param name="contain_pssm_scores_type" value="yes" /> + <conditional name="contain_pssm_scores"> + <param name="contain_pssm_scores_type" value="yes" /> + </conditional> <output name="outfile" file="empty_file.dat" ftype="blastdbd" > <extra_files type="file" value="cd00003_and_cd00008.phr" name="blastdb.phr" /> <extra_files type="file" value="cd00003_and_cd00008.pin" name="blastdb.pin" compare="sim_size" delta="8" /> @@ -116,13 +118,6 @@ .. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/ - -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations" /> </tool> |
| b |
| diff -r cc1ab05a5588 -r 491dc0cd6a0d tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Mon Dec 19 09:36:39 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Wed Mar 26 16:42:53 2025 +0000 |
| [ |
| @@ -4,9 +4,8 @@ <token name="@BINARY@">deltablast</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="parallelism" /> <expand macro="preamble" /> - <command detect_errors="aggressive"> + <command detect_errors="aggressive"><![CDATA[ ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces rpsblast @@ -26,7 +25,7 @@ @ADV_WINDOW_SIZE@ ## End of advanced options: #end if - </command> + ]]></command> <inputs> <expand macro="prot_query" /> @@ -47,18 +46,20 @@ </inputs> <outputs> <data name="output1" format="tabular" label="rpsblast on ${on_string}"> - <expand macro="output_change_format" /> - </data> </outputs> <tests> <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" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="db" /> + <param name="database" value="cd00003_and_cd00008" /> + </conditional> <param name="evalue_cutoff" value="1e-8" /> - <param name="out_format" value="6" /> + <conditional name="output"> + <param name="out_format" value="6" /> + </conditional> <output name="output1" file="empty_file.dat" ftype="tabular" /> </test> </tests> @@ -109,14 +110,6 @@ @CLI_OPTIONS@ -------- - -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations" /> </tool> |
| b |
| diff -r cc1ab05a5588 -r 491dc0cd6a0d tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Mon Dec 19 09:36:39 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Wed Mar 26 16:42:53 2025 +0000 |
| [ |
| @@ -4,9 +4,8 @@ <token name="@BINARY@">rpstblastn</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="parallelism" /> <expand macro="preamble" /> - <command detect_errors="aggressive"> + <command detect_errors="aggressive"><![CDATA[ ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces rpstblastn @@ -26,7 +25,7 @@ @ADV_QCOV_HSP_PERC@ ## End of advanced options: #end if - </command> + ]]></command> <inputs> <expand macro="nucl_query" /> @@ -53,10 +52,14 @@ <tests> <test> <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="db" /> - <param name="database" value="cd00003_and_cd00008" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="db" /> + <param name="database" value="cd00003_and_cd00008" /> + </conditional> <param name="evalue_cutoff" value="1e-8" /> - <param name="out_format" value="6" /> + <conditional name="output"> + <param name="out_format" value="6" /> + </conditional> <output name="output1" file="empty_file.dat" ftype="tabular" /> </test> </tests> @@ -107,14 +110,6 @@ @CLI_OPTIONS@ -------- - -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations" /> </tool> |
| b |
| diff -r cc1ab05a5588 -r 491dc0cd6a0d tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml Mon Dec 19 09:36:39 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml Wed Mar 26 16:42:53 2025 +0000 |
| [ |
| @@ -5,7 +5,7 @@ <import>ncbi_macros.xml</import> </macros> <expand macro="preamble" /> - <command detect_errors="aggressive"> + <command detect_errors="aggressive"><![CDATA[ ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces segmasker @@ -21,7 +21,7 @@ -locut $locut -hicut $hicut -outfmt $outformat - </command> + ]]></command> <inputs> <expand macro="input_conditional_protein_db" /> <param name="window" type="integer" value="12" label="SEG window length" help="(-window)" /> @@ -51,8 +51,10 @@ </outputs> <tests> <test> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + </conditional> <param name="window" value="12" /> <param name="locut" value="2.2" /> <param name="hicut" value="2.5" /> @@ -60,8 +62,10 @@ <output name="outfile" file="segmasker_four_human.fasta" /> </test> <test> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + </conditional> <param name="window" value="12" /> <param name="locut" value="2.2" /> <param name="hicut" value="2.5" /> @@ -69,8 +73,10 @@ <output name="outfile" file="segmasker_four_human.maskinfo-asn1-binary" /> </test> <test> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + </conditional> <param name="window" value="12" /> <param name="locut" value="2.2" /> <param name="hicut" value="2.5" /> @@ -90,12 +96,6 @@ .. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/ .. _SEG: https://www.ncbi.nlm.nih.gov/pubmed/8743706 -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations" /> </tool> |
| b |
| diff -r cc1ab05a5588 -r 491dc0cd6a0d tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Mon Dec 19 09:36:39 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Wed Mar 26 16:42:53 2025 +0000 |
| [ |
| b'@@ -4,9 +4,8 @@\n <token name="@BINARY@">tblastn</token>\n <import>ncbi_macros.xml</import>\n </macros>\n- <expand macro="parallelism" />\n <expand macro="preamble" />\n- <command detect_errors="aggressive">\n+ <command detect_errors="aggressive"><![CDATA[\n ## The command is a Cheetah template which allows some Python based syntax.\n ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces\n tblastn\n@@ -31,7 +30,7 @@\n @ADV_COMP_BASED_STATS@\n ## End of advanced options:\n #end if\n- </command>\n+ ]]></command>\n <inputs>\n <expand macro="prot_query" />\n \n@@ -72,80 +71,120 @@\n <tests>\n <test>\n <param name="query" value="four_human_proteins.fasta" ftype="fasta" />\n- <param name="db_opts_selector" value="file" />\n- <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />\n- <param name="database" value="" />\n+ <conditional name="db_opts">\n+ <param name="db_opts_selector" value="file" />\n+ <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />\n+ <param name="database" value="" />\n+ </conditional>\n <param name="evalue_cutoff" value="1e-10" />\n- <param name="out_format" value="5" />\n- <param name="adv_opts_selector" value="advanced" />\n- <param name="filter_query" value="false" />\n- <param name="matrix" value="BLOSUM80" />\n- <param name="max_hits" value="0" />\n- <param name="word_size" value="" />\n- <param name="parse_deflines" value="false" />\n+ <conditional name="output">\n+ <param name="out_format" value="5" />\n+ </conditional>\n+ <conditional name="adv_opts">\n+ <param name="adv_opts_selector" value="advanced" />\n+ <param name="filter_query" value="false" />\n+ <conditional name="matrix_gapcosts">\n+ <param name="matrix" value="BLOSUM80" />\n+ </conditional>\n+ <param name="max_hits" value="0" />\n+ <!-- <param name="word_size" value="" /> https://github.com/galaxyproject/galaxy/issues/19908 -->\n+ <param name="parse_deflines" value="false" />\n+ </conditional>\n <output name="output1" file="tblastn_four_human_vs_rhodopsin.xml" ftype="blastxml" />\n </test>\n <test>\n <param name="query" value="four_human_proteins.fasta" ftype="fasta" />\n- <param name="db_opts_selector" value="file" />\n- <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />\n- <param name="database" value="" />\n+ <conditional name="db_opts">\n+ <param name="db_opts_selector" value="file" />\n+ <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />\n+ <param name="database" value="" />\n+ </conditional>\n <param name="evalue_cutoff" value="1e-10" />\n- <param name="out_format" value="ext" />\n- <param name="adv_opts_selector" value="advanced" />\n- <param name="filter_query" value="false" />\n- <param name="matrix" value="BLOSUM80" />\n- <param name="max_hits" value="0" />\n- <param name="word_size" value="" />\n- <param name="parse_deflines" value="false" />\n+ <conditional name="output">\n+ <param name="out_format" value="ext" />\n+ </conditional>\n+ <conditional name="adv_opts">\n+ <param name="adv_opts_selector" value="advanced" />\n+ <param name="filter_query" value="false" />\n+ <conditional name="matrix_gapcosts">\n+ <param name="matrix" value="BLOSUM80" />\n+ </conditional>\n+ <param name="max_hits" value="0" />\n+ <!'..b'nes -->\n <!-- Note back on BLAST 2.2.25+ - 2.2.27+ made no difference -->\n <param name="query" value="four_human_proteins.fasta" ftype="fasta" />\n- <param name="db_opts_selector" value="file" />\n- <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />\n- <param name="database" value="" />\n+ <conditional name="db_opts">\n+ <param name="db_opts_selector" value="file" />\n+ <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />\n+ <param name="database" value="" />\n+ </conditional>\n <param name="evalue_cutoff" value="1e-10" />\n- <param name="out_format" value="6" />\n- <param name="adv_opts_selector" value="advanced" />\n- <param name="filter_query" value="false" />\n- <param name="matrix" value="BLOSUM80" />\n- <param name="max_hits" value="0" />\n- <param name="word_size" value="" />\n- <param name="parse_deflines" value="true" />\n+ <conditional name="output">\n+ <param name="out_format" value="6" />\n+ </conditional>\n+ <conditional name="adv_opts">\n+ <param name="adv_opts_selector" value="advanced" />\n+ <param name="filter_query" value="false" />\n+ <conditional name="matrix_gapcosts">\n+ <param name="matrix" value="BLOSUM80" />\n+ </conditional>\n+ <param name="max_hits" value="0" />\n+ <!-- <param name="word_size" value="" /> -->\n+ <param name="parse_deflines" value="true" />\n+ </conditional>\n <output name="output1" file="tblastn_four_human_vs_rhodopsin_deflines.tabular" ftype="tabular" />\n </test>\n <test>\n <!-- As of BLAST 2.5.0+ the full path appears twice, so get small diff -->\n <param name="query" value="four_human_proteins.fasta" ftype="fasta" />\n- <param name="db_opts_selector" value="file" />\n- <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />\n- <param name="database" value="" />\n+ <conditional name="db_opts">\n+ <param name="db_opts_selector" value="file" />\n+ <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />\n+ <param name="database" value="" />\n+ </conditional>\n <param name="evalue_cutoff" value="1e-10" />\n- <param name="out_format" value="0 -html" />\n- <param name="adv_opts_selector" value="advanced" />\n- <param name="filter_query" value="false" />\n- <param name="matrix" value="BLOSUM80" />\n- <param name="max_hits" value="0" />\n- <param name="word_size" value="" />\n- <param name="parse_deflines" value="false" />\n+ <conditional name="output">\n+ <param name="out_format" value="0 -html" />\n+ </conditional>\n+ <conditional name="adv_opts">\n+ <param name="adv_opts_selector" value="advanced" />\n+ <param name="filter_query" value="false" />\n+ <conditional name="matrix_gapcosts">\n+ <param name="matrix" value="BLOSUM80" />\n+ </conditional>\n+ <param name="max_hits" value="0" />\n+ <!-- <param name="word_size" value="" /> -->\n+ <param name="parse_deflines" value="false" />\n+ </conditional>\n <output name="output1" file="tblastn_four_human_vs_rhodopsin.html" ftype="html" lines_diff="10" />\n </test>\n </tests>\n@@ -168,14 +207,6 @@\n \n @CLI_OPTIONS@\n \n-------\n-\n-**References**\n-\n-If you use this Galaxy tool in work leading to a scientific publication please\n-cite the following papers:\n-\n-@REFERENCES@\n </help>\n <expand macro="blast_citations" />\n </tool>\n' |
| b |
| diff -r cc1ab05a5588 -r 491dc0cd6a0d tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Mon Dec 19 09:36:39 2022 +0000 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Wed Mar 26 16:42:53 2025 +0000 |
| [ |
| @@ -4,9 +4,8 @@ <token name="@BINARY@">tblastx</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="parallelism" /> <expand macro="preamble" /> - <command detect_errors="aggressive"> + <command detect_errors="aggressive"><![CDATA[ ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces tblastx @@ -28,7 +27,7 @@ @ADV_THRESHOLD@ ## End of advanced options: #end if - </command> + ]]></command> <inputs> <expand macro="nucl_query" /> @@ -61,12 +60,18 @@ <tests> <test> <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="database" value="" /> + <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> + </conditional> <param name="evalue_cutoff" value="1e-40" /> - <param name="out_format" value="6" /> - <param name="adv_opts_selector" value="basic" /> + <conditional name="output"> + <param name="out_format" value="6" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="basic" /> + </conditional> <output name="output1" file="tblastx_rhodopsin_vs_three_human.tabular" ftype="tabular" /> </test> </tests> @@ -89,14 +94,6 @@ @CLI_OPTIONS@ -------- - -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations" /> </tool> |