| Previous changeset 6:64be1ac21109 (2018-09-27) Next changeset 8:54f751e413f4 (2021-03-22) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit b2d290a8b609ebbc7f4b93716370143c41062ad4" |
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modified:
diamond.xml diamond_makedb.xml diamond_view.xml macros.xml repository_dependencies.xml test-data/db-wtax.dmnd test-data/db.dmnd test-data/diamond_results.daa test-data/diamond_results.pairwise test-data/diamond_results.sam test-data/diamond_results.tabular test-data/diamond_results.wtax.tabular test-data/diamond_results.xml |
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| diff -r 64be1ac21109 -r 62c9df8382c2 diamond.xml --- a/diamond.xml Thu Sep 27 06:30:30 2018 -0400 +++ b/diamond.xml Tue Dec 03 17:40:05 2019 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="bg_diamond" name="Diamond" version="@VERSION@.0"> +<tool id="bg_diamond" name="Diamond" version="@VERSION@.0" profile="19.01"> <description>alignment tool for short sequences against a protein database</description> <macros> <import>macros.xml</import> @@ -64,7 +64,7 @@ --subject-cover '$subject_cover' --block-size '$block_size' #if str($unal) == '1': - --unal 1 --un '$unalqueries' + --unal 1 --un '$unalqueries' #end if $no_self_hits #if $tax_cond.tax_select == 'file': @@ -103,7 +103,7 @@ <option value="26">Pachysolen tannophilus Nuclear Code</option> </param> <param argument="--min-orf" name="min_orf" type="integer" value="1" label="ignore translated sequences without an open reading frame of at least this length" help="By default this feature is disabled for sequences of length below 30, set to 20 for sequences of length below 100, and set to 40 otherwise. Setting this option to 1 will disable this feature" /> - + <param name="query_strand" argument="--strand" type="select" label="query strands to search" help=""> <option value="both" selected="True">Both</option> <option value="plus">Plus</option> @@ -165,7 +165,7 @@ <param argument="--masking" type="boolean" truevalue="1" falsevalue="0" checked="true" label="enable masking of low complexity regions?" help="Masked residues appear in the output as X"/> <conditional name="tax_cond"> <param name="tax_select" type="select" label="Restrict search taxonomically?" help="Any taxonomic rank can be used, and only reference sequences matching one of the specified taxon ids will be searched against"> - <option value="no">No</option> + <option value="no" selected="True">No</option> <option value="list">list of taxids entered manually</option> <option value="file">list of taxids from single column tabular file</option> </param> @@ -179,7 +179,7 @@ </conditional> <conditional name="filter_score"> <param name="filter_score_select" type="select" label="Method to filter?" help="(--evalue/--min-score)"> - <option value="evalue">Maximum e-value to report alignments</option> + <option value="evalue" selected="True">Maximum e-value to report alignments</option> <option value="min-score">Minimum bit score to report alignments</option> </param> <when value="evalue"> |
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| diff -r 64be1ac21109 -r 62c9df8382c2 diamond_makedb.xml --- a/diamond_makedb.xml Thu Sep 27 06:30:30 2018 -0400 +++ b/diamond_makedb.xml Tue Dec 03 17:40:05 2019 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="bg_diamond_makedb" name="Diamond makedb" version="@VERSION@"> +<tool id="bg_diamond_makedb" name="Diamond makedb" version="@VERSION@" profile="19.01"> <description>Build database from a FASTA file</description> <macros> <import>macros.xml</import> @@ -73,9 +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 +- 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 -- 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 +- 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 ]]> </help> |
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| diff -r 64be1ac21109 -r 62c9df8382c2 diamond_view.xml --- a/diamond_view.xml Thu Sep 27 06:30:30 2018 -0400 +++ b/diamond_view.xml Tue Dec 03 17:40:05 2019 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="bg_diamond_view" name="Diamond" version="@VERSION@"> +<tool id="bg_diamond_view" name="Diamond" version="@VERSION@" profile="19.01"> <description>generate formatted output from DAA files</description> <macros> <import>macros.xml</import> @@ -7,7 +7,7 @@ <expand macro="stdio" /> <expand macro="version_command" /> <command><![CDATA[ - ## need to link because diamont tries to open dataset_xxx.dat.daa + ## need to link because diamont tries to open dataset_xxx.dat.daa ln -s '$daa' input.daa && diamond view @@ -57,7 +57,7 @@ <param name="max_target_seqs" value="1" /> </conditional> <param name="forwardonly" value="--forwardonly" /> - <output name="blast_tabular" file="diamond_results.sam"/> + <output name="blast_tabular" file="diamond_results.sam" lines_diff="2"/> </test> </tests> |
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| diff -r 64be1ac21109 -r 62c9df8382c2 macros.xml --- a/macros.xml Thu Sep 27 06:30:30 2018 -0400 +++ b/macros.xml Tue Dec 03 17:40:05 2019 -0500 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION@">0.9.21</token> + <token name="@VERSION@">0.9.29</token> <xml name="requirements"> <requirements> @@ -9,12 +9,9 @@ <xml name="stdio"> <stdio> - <!-- disabled error detection by exit code to be able to detect oom errors by - regex, can be reenabled when https://github.com/galaxyproject/galaxy/pull/6338 is merged <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" /> - <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />--> + <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> <regex match="Failed to allocate sufficient memory." source="stderr" level="fatal_oom" /> - <regex match=".+" source="stderr" level="fatal" description=""/> </stdio> </xml> @@ -65,6 +62,11 @@ <option value="salltitles">All Subject Title(s)</option> <option value="qcovhsp">Query Coverage Per HSP</option> <option value="qtitle">Query title</option> + <option value="full_qseq">Query sequence</option> + <option value="full_sseq">Subject sequence</option> + <option value="qqual">Query quality values for the aligned part of the query</option> + <option value="full_qqual">Query quality values</option> + <option value="qstrand">Query strand</option> </param> </when> <when value="100"> |
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| diff -r 64be1ac21109 -r 62c9df8382c2 repository_dependencies.xml --- a/repository_dependencies.xml Thu Sep 27 06:30:30 2018 -0400 +++ b/repository_dependencies.xml Tue Dec 03 17:40:05 2019 -0500 |
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| @@ -1,4 +1,4 @@ -<?xml version="1.0"?> +<?xml version="1.0" ?> <repositories description="This requires the Diamond data manager."> - <repository changeset_revision="ce62d0912b10" name="data_manager_diamond_database_builder" owner="bgruening" toolshed="https://toolshed.g2.bx.psu.edu" /> -</repositories> + <repository changeset_revision="5a0d0bee4f8d" name="data_manager_diamond_database_builder" owner="bgruening" toolshed="https://toolshed.g2.bx.psu.edu"/> +</repositories> \ No newline at end of file |
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| diff -r 64be1ac21109 -r 62c9df8382c2 test-data/db-wtax.dmnd |
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| Binary file test-data/db-wtax.dmnd has changed |
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| diff -r 64be1ac21109 -r 62c9df8382c2 test-data/db.dmnd |
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| Binary file test-data/db.dmnd has changed |
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| diff -r 64be1ac21109 -r 62c9df8382c2 test-data/diamond_results.daa |
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| Binary file test-data/diamond_results.daa has changed |
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| diff -r 64be1ac21109 -r 62c9df8382c2 test-data/diamond_results.pairwise --- a/test-data/diamond_results.pairwise Thu Sep 27 06:30:30 2018 -0400 +++ b/test-data/diamond_results.pairwise Tue Dec 03 17:40:05 2019 -0500 |
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| @@ -8,7 +8,7 @@ >gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus] Length=284 - Score = 541.2 bits (1393), Expect = 2.0e-158 + Score = 547.4 bits (1409), Expect = 2.7e-160 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 TSDSDKIPFHPYYTIKDFLGLXXXXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPE 537 - TSDSDKIPFHPYYTIKDFLGLXXXXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPE -Sbjct 121 TSDSDKIPFHPYYTIKDFLGLXXXXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPE 180 +Query 358 TSDSDKIPFHPYYTIKDFLGLLILXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPE 537 + TSDSDKIPFHPYYTIKDFLGLLILXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPE +Sbjct 121 TSDSDKIPFHPYYTIKDFLGLLILXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPE 180 Query 538 WYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMD 717 WYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMD |
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| diff -r 64be1ac21109 -r 62c9df8382c2 test-data/diamond_results.sam --- a/test-data/diamond_results.sam Thu Sep 27 06:30:30 2018 -0400 +++ b/test-data/diamond_results.sam Tue Dec 03 17:40:05 2019 -0500 |
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| @@ -1,6 +1,6 @@ @HD VN:1.5 SO:query -@PG PN:DIAMOND +@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 @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 +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 |
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| diff -r 64be1ac21109 -r 62c9df8382c2 test-data/diamond_results.tabular --- a/test-data/diamond_results.tabular Thu Sep 27 06:30:30 2018 -0400 +++ b/test-data/diamond_results.tabular Tue Dec 03 17:40:05 2019 -0500 |
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| @@ -1,2 +1,2 @@ -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 +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 |
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| diff -r 64be1ac21109 -r 62c9df8382c2 test-data/diamond_results.wtax.tabular --- a/test-data/diamond_results.wtax.tabular Thu Sep 27 06:30:30 2018 -0400 +++ b/test-data/diamond_results.wtax.tabular Tue Dec 03 17:40:05 2019 -0500 |
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| @@ -1,1 +1,1 @@ -sequence gi|5524211|gb|AAD44166.1| 99.6 284 0 1 1 283 1 284 2.0e-158 541.2 +sequence gi|5524211|gb|AAD44166.1| 99.6 284 0 1 1 283 1 284 2.7e-160 547.4 |
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| diff -r 64be1ac21109 -r 62c9df8382c2 test-data/diamond_results.xml --- a/test-data/diamond_results.xml Thu Sep 27 06:30:30 2018 -0400 +++ b/test-data/diamond_results.xml Tue Dec 03 17:40:05 2019 -0500 |
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| @@ -2,9 +2,9 @@ <!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>diamond 0.9.21</BlastOutput_version> + <BlastOutput_version>diamond 0.9.29</BlastOutput_version> <BlastOutput_reference>Benjamin Buchfink, Xie Chao, and Daniel Huson (2015), "Fast and sensitive protein alignment using DIAMOND", Nature Methods 12:59-60.</BlastOutput_reference> - <BlastOutput_db>.dmnd</BlastOutput_db> + <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>Query_1</BlastOutput_query-ID> <BlastOutput_query-def>sequence</BlastOutput_query-def> <BlastOutput_query-len>283</BlastOutput_query-len> @@ -33,9 +33,9 @@ <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> - <Hsp_bit-score>541.2</Hsp_bit-score> - <Hsp_score>1393</Hsp_score> - <Hsp_evalue>2.0e-158</Hsp_evalue> + <Hsp_bit-score>547.4</Hsp_bit-score> + <Hsp_score>1409</Hsp_score> + <Hsp_evalue>2.7e-160</Hsp_evalue> <Hsp_query-from>1</Hsp_query-from> <Hsp_query-to>284</Hsp_query-to> <Hsp_hit-from>1</Hsp_hit-from> @@ -46,9 +46,9 @@ <Hsp_positive>283</Hsp_positive> <Hsp_gaps>1</Hsp_gaps> <Hsp_align-len>284</Hsp_align-len> - <Hsp_qseq>LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFIL-FTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLXXXXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY</Hsp_qseq> - <Hsp_hseq>LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLXXXXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY</Hsp_hseq> - <Hsp_midline>LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFIL FTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLXXXXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY</Hsp_midline> + <Hsp_qseq>LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFIL-FTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLLILXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY</Hsp_qseq> + <Hsp_hseq>LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLLILXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY</Hsp_hseq> + <Hsp_midline>LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFIL FTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLLILXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY</Hsp_midline> </Hsp> </Hit_hsps> </Hit> |