# HG changeset patch # User iuc # Date 1616419283 0 # Node ID 54f751e413f4b78bee1832e4788605f7884d9156 # Parent 62c9df8382c204088f52ab53b33a8edc18909ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" diff -r 62c9df8382c2 -r 54f751e413f4 diamond.xml --- a/diamond.xml Tue Dec 03 17:40:05 2019 -0500 +++ b/diamond.xml Mon Mar 22 13:21:23 2021 +0000 @@ -6,7 +6,7 @@ - + + + + + + + + + + + + + + + @@ -139,16 +151,45 @@ - + - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -161,7 +202,6 @@ - @@ -171,7 +211,10 @@ - + + [0-9,]* + not ("0" in value.split(",") or "1" in value.split(",")) + @@ -193,7 +236,6 @@ - @@ -210,13 +252,15 @@ - + - + - + + + @@ -230,7 +274,9 @@ - + + + @@ -243,14 +289,16 @@ - - + + - + + + @@ -264,7 +312,9 @@ - + + + @@ -282,7 +332,9 @@ - + + + @@ -291,12 +343,14 @@ - - + + - + + + @@ -313,6 +367,42 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + @@ -33,6 +34,7 @@ + @@ -53,6 +55,7 @@ + @@ -73,7 +76,9 @@ .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/ -- taxonmap: Path to mapping file that maps NCBI protein accession numbers to taxon ids (gzip compressed). This parameter is optional and needs to be supplied in order to provide taxonomy features. The file can be downloaded from NCBI: ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz +- taxonmap: Path to mapping file that maps NCBI protein accession numbers to taxon ids (gzip compressed). This parameter is optional and needs to be supplied in order to provide taxonomy features. The file can be downloaded from NCBI: ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.FULL.gz + +- taxonnames: Path to the names.dmp file from the NCBI taxonomy. This parameter is optional and needs to be supplied in order to provide taxonomy features. The file is contained within this archive downloadable at NCBI: ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip - taxonnodes: Path to the nodes.dmp file from the NCBI taxonomy. This parameter is optional and needs to be supplied in order to provide taxonomy features. The file is contained within this archive downloadable at NCBI: ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip ]]> diff -r 62c9df8382c2 -r 54f751e413f4 diamond_view.xml --- a/diamond_view.xml Tue Dec 03 17:40:05 2019 -0500 +++ b/diamond_view.xml Mon Mar 22 13:21:23 2021 +0000 @@ -1,4 +1,4 @@ - + generate formatted output from DAA files macros.xml @@ -6,11 +6,12 @@ - - + - + diff -r 62c9df8382c2 -r 54f751e413f4 macros.xml --- a/macros.xml Tue Dec 03 17:40:05 2019 -0500 +++ b/macros.xml Mon Mar 22 13:21:23 2021 +0000 @@ -1,5 +1,5 @@ - 0.9.29 + 2.0.8 @@ -9,14 +9,12 @@ - - - + - diamond version + diamond version | cut -d" " -f 3 @@ -30,7 +28,7 @@ - + @@ -52,12 +50,13 @@ + - + @@ -67,13 +66,15 @@ + + - + @@ -97,6 +98,14 @@ + + + + + + + + 10.1038/nmeth.3176 @@ -115,7 +124,7 @@ output["outfmt"] == "6" - + output["outfmt"] == "100" @@ -153,6 +162,6 @@ --max-target-seqs '$hit_filter.max_target_seqs' #else: --top '$hit_filter.top' - #end if + #end if diff -r 62c9df8382c2 -r 54f751e413f4 repository_dependencies.xml --- a/repository_dependencies.xml Tue Dec 03 17:40:05 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ - - - - \ No newline at end of file diff -r 62c9df8382c2 -r 54f751e413f4 test-data/db-wtax.dmnd Binary file test-data/db-wtax.dmnd has changed diff -r 62c9df8382c2 -r 54f751e413f4 test-data/db.dmnd Binary file test-data/db.dmnd has changed diff -r 62c9df8382c2 -r 54f751e413f4 test-data/diamond_database.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/diamond_database.loc Mon Mar 22 13:21:23 2021 +0000 @@ -0,0 +1,1 @@ +testDb test_index ${__HERE__}/db.dmnd diff -r 62c9df8382c2 -r 54f751e413f4 test-data/diamond_results.daa Binary file test-data/diamond_results.daa has changed diff -r 62c9df8382c2 -r 54f751e413f4 test-data/diamond_results.pairwise --- a/test-data/diamond_results.pairwise Tue Dec 03 17:40:05 2019 -0500 +++ b/test-data/diamond_results.pairwise Mon Mar 22 13:21:23 2021 +0000 @@ -8,7 +8,7 @@ >gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus] Length=284 - Score = 547.4 bits (1409), Expect = 2.7e-160 + Score = 550 bits (1417), Expect = 1.44e-205 Identities = 283/284 (99%), Positives = 283/284 (99%), Gaps = 1/284 (0%) Frame = 1 @@ -20,9 +20,9 @@ AIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFIL FTMVALAGVHLTFLHETGSNNPLGL Sbjct 61 AIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGL 120 -Query 358 TSDSDKIPFHPYYTIKDFLGLLILXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPE 537 - TSDSDKIPFHPYYTIKDFLGLLILXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPE -Sbjct 121 TSDSDKIPFHPYYTIKDFLGLLILXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPE 180 +Query 358 TSDSDKIPFHPYYTIKDFLGLLILXXXXXXXALLSPDMLGDPDNHMPADPLNTPLHIKPE 537 + TSDSDKIPFHPYYTIKDFLGLLILXXXXXXXALLSPDMLGDPDNHMPADPLNTPLHIKPE +Sbjct 121 TSDSDKIPFHPYYTIKDFLGLLILXXXXXXXALLSPDMLGDPDNHMPADPLNTPLHIKPE 180 Query 538 WYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMD 717 WYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMD diff -r 62c9df8382c2 -r 54f751e413f4 test-data/diamond_results.sam --- a/test-data/diamond_results.sam Tue Dec 03 17:40:05 2019 -0500 +++ b/test-data/diamond_results.sam Mon Mar 22 13:21:23 2021 +0000 @@ -1,6 +1,6 @@ @HD VN:1.5 SO:query -@PG PN:DIAMOND VN:0.9.29 CL:diamond view --daa input.daa --outfmt 101 --out /tmp/tmpgnYFop/files/3/3/7/dataset_3370e74a-4639-49d2-b5de-fe40b7c3b66a.dat --top 0 --forwardonly --compress 0 +@PG PN:DIAMOND VN:2.0.8 CL:diamond view --threads 1 --daa input.daa --outfmt 101 --out /tmp/tmpz1aqzru3/files/3/f/6/dataset_3f6f43ac-3af2-4ec2-93be-9ced0e692b43.dat --top 0 --forwardonly --compress 0 @mm BlastP @CO BlastP-like alignments @CO Reporting AS: bitScore, ZR: rawScore, ZE: expected, ZI: percent identity, ZL: reference length, ZF: frame, ZS: query start DNA coordinate -sequence 0 gi|5524211|gb|AAD44166.1| 1 255 94M1D189M * 0 0 LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFILFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLLILXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY * AS:i:547 NM:i:1 ZL:i:284 ZR:i:1409 ZE:f:2.7e-160 ZI:i:99 ZF:i:1 ZS:i:1 MD:Z:94^P189 +sequence 0 gi|5524211|gb|AAD44166.1| 1 255 94M1D189M * 0 0 LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFILFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLLILXXXXXXXALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY * AS:i:550 NM:i:1 ZL:i:284 ZR:i:1417 ZE:f:1.44e-205 ZI:i:99 ZF:i:1 ZS:i:1 MD:Z:94^P189 diff -r 62c9df8382c2 -r 54f751e413f4 test-data/diamond_results.tabular --- a/test-data/diamond_results.tabular Tue Dec 03 17:40:05 2019 -0500 +++ b/test-data/diamond_results.tabular Mon Mar 22 13:21:23 2021 +0000 @@ -1,2 +1,2 @@ -sequence gi|5524211|gb|AAD44166.1| 99.6 284 0 1 1 283 1 284 2.7e-160 547.4 -sequence gi|5524212|gb|AAD44167.1| 79.2 284 58 1 1 283 1 284 1.1e-116 402.5 +sequence gi|5524211|gb|AAD44166.1| 99.6 284 0 1 1 283 1 284 1.44e-205 550 94M1D189M 100 0 0 0 +sequence gi|5524212|gb|AAD44167.1| 79.6 284 57 1 1 283 1 284 5.77e-150 409 105M1D178M 100 0 0 0 diff -r 62c9df8382c2 -r 54f751e413f4 test-data/diamond_results.wtax.tabular --- a/test-data/diamond_results.wtax.tabular Tue Dec 03 17:40:05 2019 -0500 +++ b/test-data/diamond_results.wtax.tabular Mon Mar 22 13:21:23 2021 +0000 @@ -1,1 +1,1 @@ -sequence gi|5524211|gb|AAD44166.1| 99.6 284 0 1 1 283 1 284 2.7e-160 547.4 +sequence gi|5524211|gb|AAD44166.1| 99.6 284 0 1 1 283 1 284 1.44e-205 550 diff -r 62c9df8382c2 -r 54f751e413f4 test-data/diamond_results.xml --- a/test-data/diamond_results.xml Tue Dec 03 17:40:05 2019 -0500 +++ b/test-data/diamond_results.xml Mon Mar 22 13:21:23 2021 +0000 @@ -2,7 +2,7 @@ blastp - diamond 0.9.29 + diamond 2.0.8 Benjamin Buchfink, Xie Chao, and Daniel Huson (2015), "Fast and sensitive protein alignment using DIAMOND", Nature Methods 12:59-60. Query_1 @@ -33,11 +33,11 @@ 1 - 547.4 - 1409 - 2.7e-160 + 550 + 1417 + 1.44e-205 1 - 284 + 283 1 284 0 @@ -46,9 +46,9 @@ 283 1 284 - LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFIL-FTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLLILXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY - LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLLILXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY - LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFIL FTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLLILXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY + LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFIL-FTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLLILXXXXXXXALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY + LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLLILXXXXXXXALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY + LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFIL FTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLLILXXXXXXXALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY diff -r 62c9df8382c2 -r 54f751e413f4 test-data/diamond_view_results.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/diamond_view_results.tabular Mon Mar 22 13:21:23 2021 +0000 @@ -0,0 +1,2 @@ +sequence gi|5524211|gb|AAD44166.1| 99.6 284 0 1 1 283 1 284 1.44e-205 550 94M1D189M 100 +sequence gi|5524212|gb|AAD44167.1| 79.6 284 57 1 1 283 1 284 5.77e-150 409 83M1D200M 100 diff -r 62c9df8382c2 -r 54f751e413f4 test-data/names.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/names.dmp Mon Mar 22 13:21:23 2021 +0000 @@ -0,0 +1,11 @@ +1 | all | | synonym | +1 | root | | scientific name | +2 | Bacteria | Bacteria | scientific name | +2 | bacteria | | blast name | +2 | eubacteria | | genbank common name | +2 | Monera | Monera | in-part | +3 | Procaryotae | Procaryotae | in-part | +3 | Prokaryotae | Prokaryotae | in-part | +3 | Prokaryota | Prokaryota | in-part | +3 | prokaryote | prokaryote | in-part | +3 | prokaryotes | prokaryotes | in-part | diff -r 62c9df8382c2 -r 54f751e413f4 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Mon Mar 22 13:21:23 2021 +0000 @@ -0,0 +1,7 @@ + + + + value, name, db_path + +
+