# HG changeset patch # User bgruening # Date 1538044197 14400 # Node ID 409ecbc3155833e2875f73741babe4fda2e2c7bb # Parent b9c935b2339965d72e499d16d60877a07952828f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 diff -r b9c935b23399 -r 409ecbc31558 diamond.xml --- a/diamond.xml Tue Aug 08 16:33:35 2017 -0400 +++ b/diamond.xml Thu Sep 27 06:29:57 2018 -0400 @@ -1,4 +1,4 @@ - + alignment tool for short sequences against a protein database macros.xml @@ -18,26 +18,21 @@ && diamond - $method_select.method_select + $method_cond.method_select --threads "\${GALAXY_SLOTS:-12}" --db ./database --query '$query' - #if $method_select.method_select == "blastx" - --query-gencode '$query_gencode' + #if $method_cond.method_select == "blastx" + --query-gencode '$method_cond.query_gencode' + --strand '$method_cond.query_strand' + --min-orf $method_cond.min_orf + #if $method_cond.frameshift_cond.frameshift_select == 'yes' + --frameshift $method_cond.frameshift_cond.frameshift + $method_cond.frameshift_cond.range_culling + #end if #end if - #if $output.outfmt == "5" - --outfmt '5' - --out '$blast_xml' - $output.salltitles - #else if $output.outfmt == "6" - --outfmt '6' #echo ' '.join(str($output.fields).split(',')) - --out '$blast_tabular' - #else if $output.outfmt == "101" - --outfmt '101' - --out '$sam_output' - $output.salltitles - #end if + @OUTPUT_ARGS@ --compress '0' #if $sensitivity == "1" @@ -46,16 +41,17 @@ --more-sensitive #end if - --gapopen '$gapopen' - --gapextend '$gapextend' + #if str($gapopen) != "": + --gapopen '$gapopen' + #end if + #if str($gapextend) != "": + --gapextend '$gapextend' + #end if --matrix '$matrix' - --seg '$seg' + --comp-based-stats '$comp_based_stats' + --masking '$masking' - #if str($hit_filter.hit_filter_select) == 'max': - --max-target-seqs '$hit_filter.max_target_seqs' - #else: - --top '$hit_filter.top' - #end if + @HITFILTER_ARGS@ #if str($filter_score.filter_score_select) == 'evalue': --evalue '$filter_score.evalue' @@ -65,131 +61,120 @@ --id '$id' --query-cover '$query_cover' + --subject-cover '$subject_cover' --block-size '$block_size' + #if str($unal) == '1': + --unal 1 --un '$unalqueries' + #end if + $no_self_hits + #if $tax_cond.tax_select == 'file': + --taxonlist `cat '$tax_cond.taxonlistfile' | grep -v "^#" | grep -v "^$" | tr "\n" "," | sed 's/,$//'` + #else if $tax_cond.tax_select == 'list': + --taxonlist '$tax_cond.taxonlist' + #end if ]]> - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + - - + + - - - - + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + - - + + + - - + + @@ -204,47 +189,131 @@ + + + - - - output["outfmt"] == "5" - - - output["outfmt"] == "6" - - - output["outfmt"] == "101" + + + unal == "1" - - + + + - - - - + + + + + + + + - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + #if str($tax_cond.tax_select) == 'yes': + --taxonmap '$tax_cond.taxonmap' + --taxonnodes '$tax_cond.taxonnodes' + #end if + ]]> - + + + + + + + + + + + + @@ -29,7 +45,16 @@ - + + + + + + + + + + @@ -48,6 +73,9 @@ .. _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://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz + +- 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://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip ]]> diff -r b9c935b23399 -r 409ecbc31558 diamond_view.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/diamond_view.xml Thu Sep 27 06:29:57 2018 -0400 @@ -0,0 +1,98 @@ + + generate formatted output from DAA files + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r b9c935b23399 -r 409ecbc31558 macros.xml --- a/macros.xml Tue Aug 08 16:33:35 2017 -0400 +++ b/macros.xml Thu Sep 27 06:29:57 2018 -0400 @@ -1,5 +1,5 @@ - 0.8.24 + 0.9.21 @@ -9,6 +9,12 @@ + + + @@ -16,9 +22,135 @@ diamond version + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.1038/nmeth.3176 + + + + + output["outfmt"] == "0" + + + output["outfmt"] == "5" + + + output["outfmt"] == "6" + + + + output["outfmt"] == "100" + + + output["outfmt"] == "101" + + + output["outfmt"] == "102" + + + + + #if $output.outfmt == "0" + --outfmt '0' + --out '$blast_pairw' + #else if $output.outfmt == "5" + --outfmt '5' + --out '$blast_xml' + #else if $output.outfmt == "6" + --outfmt '6' #echo ' '.join(str($output.fields).split(',')) + --out '$blast_tabular' + #else if $output.outfmt == "100" + --outfmt '100' + --out output.daa + #else if $output.outfmt == "101" + --outfmt '101' + --out '$sam_output' + #else if $output.outfmt == "102" + --outfmt '102' + --out '$tax_output' + #end if + + + + #if str($hit_filter.hit_filter_select) == 'max': + --max-target-seqs '$hit_filter.max_target_seqs' + #else: + --top '$hit_filter.top' + #end if + diff -r b9c935b23399 -r 409ecbc31558 test-data/db-wtax.dmnd Binary file test-data/db-wtax.dmnd has changed diff -r b9c935b23399 -r 409ecbc31558 test-data/db.dmnd Binary file test-data/db.dmnd has changed diff -r b9c935b23399 -r 409ecbc31558 test-data/db.fasta --- a/test-data/db.fasta Tue Aug 08 16:33:35 2017 -0400 +++ b/test-data/db.fasta Thu Sep 27 06:29:57 2018 -0400 @@ -4,3 +4,9 @@ LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX IENY +>gi|5524212|gb|AAD44167.1| cytochrome c [Elephas minimus minimus] +LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAGGGGGGGWGQMSFWGATVITNLFSAIPYIGTNLV +EWIWGGFSVDKAAAAAAAAAAAAAAAAAAAAAAAAATFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG +LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL +GLMPFLHTSKHRSMMLRPLSQALAAAAAAAAAAAAAAAAAAAAAAATIIGQMASILYFSIILAFLPIAGX +IENY diff -r b9c935b23399 -r 409ecbc31558 test-data/diamond_results.daa Binary file test-data/diamond_results.daa has changed diff -r b9c935b23399 -r 409ecbc31558 test-data/diamond_results.pairwise --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/diamond_results.pairwise Thu Sep 27 06:29:57 2018 -0400 @@ -0,0 +1,34 @@ +BLASTP 2.3.0+ + + +Query= sequence more text + +Length=849 + +>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus] +Length=284 + + Score = 541.2 bits (1393), Expect = 2.0e-158 + Identities = 283/284 (99%), Positives = 283/284 (99%), Gaps = 1/284 (0%) + Frame = 1 + +Query 1 LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFS 180 + LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFS +Sbjct 1 LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFS 60 + +Query 181 AIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFIL-FTMVALAGVHLTFLHETGSNNPLGL 357 + AIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFIL FTMVALAGVHLTFLHETGSNNPLGL +Sbjct 61 AIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGL 120 + +Query 358 TSDSDKIPFHPYYTIKDFLGLXXXXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPE 537 + TSDSDKIPFHPYYTIKDFLGLXXXXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPE +Sbjct 121 TSDSDKIPFHPYYTIKDFLGLXXXXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPE 180 + +Query 538 WYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMD 717 + WYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMD +Sbjct 181 WYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMD 240 + +Query 718 LLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY 849 + LLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY +Sbjct 241 LLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY 284 + diff -r b9c935b23399 -r 409ecbc31558 test-data/diamond_results.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/diamond_results.sam Thu Sep 27 06:29:57 2018 -0400 @@ -0,0 +1,6 @@ +@HD VN:1.5 SO:query +@PG PN:DIAMOND +@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 LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFILFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLXXXXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY * AS:i:541 NM:i:1 ZL:i:284 ZR:i:1393 ZE:f:2.0e-158 ZI:i:99 ZF:i:1 ZS:i:1 MD:Z:94^P189 diff -r b9c935b23399 -r 409ecbc31558 test-data/diamond_results.tabular --- a/test-data/diamond_results.tabular Tue Aug 08 16:33:35 2017 -0400 +++ b/test-data/diamond_results.tabular Thu Sep 27 06:29:57 2018 -0400 @@ -1,1 +1,2 @@ -sequence gi|5524211|gb|AAD44166.1| 90.5 284 26 1 1 283 1 284 1.0e-152 521.2 +sequence gi|5524211|gb|AAD44166.1| 99.6 284 0 1 1 283 1 284 2.0e-158 541.2 +sequence gi|5524212|gb|AAD44167.1| 74.6 284 71 1 1 283 1 284 1.3e-106 369.0 diff -r b9c935b23399 -r 409ecbc31558 test-data/diamond_results.wtax.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/diamond_results.wtax.tabular Thu Sep 27 06:29:57 2018 -0400 @@ -0,0 +1,1 @@ +sequence gi|5524211|gb|AAD44166.1| 99.6 284 0 1 1 283 1 284 2.0e-158 541.2 diff -r b9c935b23399 -r 409ecbc31558 test-data/diamond_results.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/diamond_results.xml Thu Sep 27 06:29:57 2018 -0400 @@ -0,0 +1,69 @@ + + + + blastp + diamond 0.9.21 + Benjamin Buchfink, Xie Chao, and Daniel Huson (2015), "Fast and sensitive protein alignment using DIAMOND", Nature Methods 12:59-60. + .dmnd + Query_1 + sequence + 283 + + + blosum62 + 0.001 + 11 + 1 + F + + + + + 1 + Query_1 + sequence + 283 + + + 1 + gi|5524211|gb|AAD44166.1| + + AAD44166.1 + 284 + + + 1 + 541.2 + 1393 + 2.0e-158 + 1 + 284 + 1 + 284 + 0 + 0 + 283 + 283 + 1 + 284 + LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFIL-FTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLXXXXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY + LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLXXXXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY + LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFIL FTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLXXXXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY + + + + + + + 2 + 568 + 0 + 0 + 0.041000 + 0.267000 + 0 + + + + + \ No newline at end of file diff -r b9c935b23399 -r 409ecbc31558 test-data/nodes.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nodes.dmp Thu Sep 27 06:29:57 2018 -0400 @@ -0,0 +1,3 @@ +1 | 1 | no rank | | 8 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | | +2 | 1 | species | AC | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | +3 | 1 | species | AC | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | diff -r b9c935b23399 -r 409ecbc31558 test-data/nucleotide.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nucleotide.fasta Thu Sep 27 06:29:57 2018 -0400 @@ -0,0 +1,17 @@ +>sequence more text +CTGTGCCTGTACACCCACATCGGCAGAAACATCTACTACGGCAGCTACCTGTACAGCGAG +ACCTGGAACACCGGCATCATGCTGCTGCTGATCACCATGGCCACCGCCTTCATGGGCTAC +GTGCTGCCCTGGGGCCAGATGAGCTTCTGGGGCGCCACCGTGATCACCAACCTGTTCAGC +GCCATCCCCTACATCGGCACCAACCTGGTGGAGTGGATCTGGGGCGGCTTCAGCGTGGAC +AAGGCCACCCTGAACAGATTCTTCGCCTTCCACTTCATCCTGTTCACCATGGTGGCCCTG +GCCGGCGTGCACCTGACCTTCCTGCACGAGACCGGCAGCAACAACCCCCTGGGCCTGACC +AGCGACAGCGACAAGATCCCCTTCCACCCCTACTACACCATCAAGGACTTCCTGGGCCTG +CTGATCCTGATCCTGCTGCTGCTGCTGCTGGCCCTGCTGAGCCCCGACATGCTGGGCGAC +CCCGACAACCACATGCCCGCCGACCCCCTGAACACCCCCCTGCACATCAAGCCCGAGTGG +TACTTCCTGTTCGCCTACGCCATCCTGAGAAGCGTGCCCAACAAGCTGGGCGGCGTGCTG +GCCCTGTTCCTGAGCATCGTGATCCTGGGCCTGATGCCCTTCCTGCACACCAGCAAGCAC +AGAAGCATGATGCTGAGACCCCTGAGCCAGGCCCTGTTCTGGACCCTGACCATGGACCTG +CTGACCCTGACCTGGATCGGCAGCCAGCCCGTGGAGTACCCCTACACCATCATCGGCCAG +ATGGCCAGCATCCTGTACTTCAGCATCATCCTGGCCTTCCTGCCCATCGCCGGCNNNATC +GAGAACTAC + diff -r b9c935b23399 -r 409ecbc31558 test-data/prot.accession2taxid --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prot.accession2taxid Thu Sep 27 06:29:57 2018 -0400 @@ -0,0 +1,4 @@ +accession accession.version taxid gi +AAD44166 AAD44166.1 2 5524211 +AAD44167 AAD44167.1 3 5524212 + diff -r b9c935b23399 -r 409ecbc31558 test-data/protein.fasta --- a/test-data/protein.fasta Tue Aug 08 16:33:35 2017 -0400 +++ b/test-data/protein.fasta Thu Sep 27 06:29:57 2018 -0400 @@ -1,4 +1,4 @@ ->sequence +>sequence more text LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV EWIWGGFSVDKATLNRFFAFHFILFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL