# HG changeset patch
# User iuc
# Date 1745330607 0
# Node ID e7d2c4ed18a569794fe50e9e86595c059b805a03
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/kaiju commit 59064c06143fdc7d7b17178e46911ba1009cd32e
diff -r 000000000000 -r e7d2c4ed18a5 kaiju2table.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/kaiju2table.xml Tue Apr 22 14:03:27 2025 +0000
@@ -0,0 +1,95 @@
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+ macros.xml
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\ No newline at end of file
diff -r 000000000000 -r e7d2c4ed18a5 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Apr 22 14:03:27 2025 +0000
@@ -0,0 +1,96 @@
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+ 1.10.1
+ 0
+ 23.2
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+ kaiju
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+ kaiju
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+ 10.1038/ncomms11257
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\ No newline at end of file
diff -r 000000000000 -r e7d2c4ed18a5 test-data/kaiju-taxnames.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kaiju-taxnames.out Tue Apr 22 14:03:27 2025 +0000
@@ -0,0 +1,1 @@
+C testseq 2697049 Severe acute respiratory syndrome coronavirus 2
diff -r 000000000000 -r e7d2c4ed18a5 test-data/kaiju-test-db/database.fmi
Binary file test-data/kaiju-test-db/database.fmi has changed
diff -r 000000000000 -r e7d2c4ed18a5 test-data/kaiju-test-db/names.dmp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kaiju-test-db/names.dmp Tue Apr 22 14:03:27 2025 +0000
@@ -0,0 +1,53 @@
+10239 | Vira | | synonym |
+10239 | Viridae | | synonym |
+10239 | viruses | | blast name |
+10239 | Viruses | | scientific name |
+11118 | Coronaviridae | | scientific name |
+58346 | CCUG 11118 | CCUG 11118 | type material |
+76804 | Nidovirales | | scientific name |
+79912 | NCIMB 11118 | NCIMB 11118 | type material |
+153721 | DSM 11118 | DSM 11118 | type material |
+457096 | MICH 11118 | MICH 11118 | type material |
+457096 | MICH-11118 | MICH-11118 | type material |
+457096 | MICH:11118 | MICH:11118 | type material |
+557004 | Matayba cf. opaca Acevedo 11118 | | scientific name |
+569542 | Nocardia sp. 11118 | | scientific name |
+652290 | Sordariomycetes sp. 11118 | | scientific name |
+682956 | CGMCC 1.10239 | CGMCC 1.10239 | type material |
+694002 | Betacoronavirus | | scientific name |
+694002 | Coronavirus | Coronavirus | in-part |
+694002 | Coronavirus group 2 | | equivalent name |
+694002 | Group 2 species | | equivalent name |
+694009 | HCoV-SARS | | acronym |
+694009 | Human coronavirus (strain SARS) | | equivalent name |
+694009 | SARS | | acronym |
+694009 | SARS-like coronavirus | | equivalent name |
+694009 | SARSr-CoV | | acronym |
+694009 | SARSrCoV | | acronym |
+694009 | SARS-related coronavirus | | equivalent name |
+694009 | Severe acute respiratory syndrome-related coronavirus | | scientific name |
+926565 | Sporocytophaga myxococcoides DSM 11118 | | scientific name |
+2268389 | Arora 11118 | Arora 11118 | type material |
+2499399 | Cornidovirineae | | scientific name |
+2501931 | Orthocoronavirinae | | scientific name |
+2509511 | Sarbecovirus | | scientific name |
+2559587 | Riboviria | | scientific name |
+2559587 | RNA viruses and retroviruses | | genbank common name |
+2559587 | RNA viruses and viroids | | common name |
+2559587 | RNA viruses | | common name |
+2697049 | 2019-nCoV | | equivalent name |
+2697049 | COVID-19 virus | | equivalent name |
+2697049 | HCoV-19 | | equivalent name |
+2697049 | Human coronavirus 2019 | | equivalent name |
+2697049 | SARS-2 | | equivalent name |
+2697049 | SARS2 | | equivalent name |
+2697049 | SARS-CoV-2 | | acronym |
+2697049 | SARS-CoV2 | | equivalent name |
+2697049 | Severe acute respiratory syndrome coronavirus 2 | | scientific name |
+2705539 | CLZhao 10239 | CLZhao 10239 | type material |
+2732396 | Orthornavirae | | scientific name |
+2732408 | Pisuviricota | | scientific name |
+2732506 | Pisoniviricetes | | scientific name |
+3093623 | FAKU:10239 | FAKU:10239 | type material |
+1 | all | | synonym |
+1 | root | | scientific name |
diff -r 000000000000 -r e7d2c4ed18a5 test-data/kaiju-test-db/nodes.dmp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kaiju-test-db/nodes.dmp Tue Apr 22 14:03:27 2025 +0000
@@ -0,0 +1,14 @@
+1 | 1 | no rank | | 8 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | |
+2697049 | 694009 | no rank | | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | |
+694009 | 2509511 | species | SA | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | code compliant; specified |
+2509511 | 694002 | subgenus | | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | code compliant |
+694002 | 2501931 | genus | | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | code compliant |
+2501931 | 11118 | subfamily | | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | code compliant |
+11118 | 2499399 | family | | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | code compliant |
+2499399 | 76804 | suborder | | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | code compliant |
+76804 | 2732506 | order | | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | code compliant |
+2732506 | 2732408 | class | | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | |
+2732408 | 2732396 | phylum | | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | |
+2732396 | 2559587 | kingdom | | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | |
+2559587 | 10239 | realm | RX | 9 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | |
+10239 | 1 | acellular root | | 9 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | |
diff -r 000000000000 -r e7d2c4ed18a5 test-data/kaiju.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kaiju.loc Tue Apr 22 14:03:27 2025 +0000
@@ -0,0 +1,1 @@
+test test name ${__HERE__}/kaiju-test-db/ 1.0
\ No newline at end of file
diff -r 000000000000 -r e7d2c4ed18a5 test-data/kaiju.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kaiju.out Tue Apr 22 14:03:27 2025 +0000
@@ -0,0 +1,1 @@
+C testseq 2697049
diff -r 000000000000 -r e7d2c4ed18a5 test-data/kaiju2krona.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kaiju2krona.out Tue Apr 22 14:03:27 2025 +0000
@@ -0,0 +1,1 @@
+1 root Viruses Riboviria Orthornavirae Pisuviricota Pisoniviricetes Nidovirales Cornidovirineae Coronaviridae Orthocoronavirinae Betacoronavirus Sarbecovirus Severe acute respiratory syndrome-related coronavirus Severe acute respiratory syndrome coronavirus 2
diff -r 000000000000 -r e7d2c4ed18a5 test-data/kaiju2table.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kaiju2table.out Tue Apr 22 14:03:27 2025 +0000
@@ -0,0 +1,4 @@
+file percent reads taxon_id taxon_name
+kaiju_out 100.000000 1 10239 Viruses
+kaiju_out 0.000000 0 NA cannot be assigned to a (non-viral) phylum
+kaiju_out 0.000000 0 NA unclassified
diff -r 000000000000 -r e7d2c4ed18a5 test-data/kaijux.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kaijux.out Tue Apr 22 14:03:27 2025 +0000
@@ -0,0 +1,1 @@
+C testseq 1918 YP_009725295.1_2697049,YP_009724389.1_2697049, RSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRANNTKGSLPINVIVFDG,
diff -r 000000000000 -r e7d2c4ed18a5 test-data/query.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/query.fa Tue Apr 22 14:03:27 2025 +0000
@@ -0,0 +1,26 @@
+>testseq
+AATGTGAAAACTACCGAAGTTGTAGGAGACATTATACTTAAACCAGCAAATAA
+TAGTTTAAAAATTACAGAAGAGGTTGGCCACACAGATCTAATGGCTGCTTATGTAGACAATTCTAGTCTT
+ACTATTAAGAAACCTAATGAATTATCTAGAGTATTAGGTTTGAAAACCCTTGCTACTCATGGTTTAGCTG
+CTGTTAATAGTGTCCCTTGGGATACTATAGCTAATTATGCTAAGCCTTTTCTTAACAAAGTTGTTAGTAC
+AACTACTAACATAGTTACACGGTGTTTAAACCGTGTTTGTACTAATTATATGCCTTATTTCTTTACTTTA
+TTGCTACAATTGTGTACTTTTACTAGAAGTACAAATTCTAGAATTAAAGCATCTATGCCGACTACTATAG
+CAAAGAATACTGTTAAGAGTGTCGGTAAATTTTGTCTAGAGGCTTCATTTAATTATTTGAAGTCACCTAA
+TTTTTCTAAACTGATAAATATTATAATTTGGTTTTTACTATTAAGTGTTTGCCTAGGTTCTTTAATCTAC
+TCAACCGCTGCTTTAGGTGTTTTAATGTCTAATTTAGGCATGCCTTCTTACTGTACTGGTTACAGAGAAG
+GCTATTTGAACTCTACTAATGTCACTATTGCAACCTACTGTACTGGTTCTATACCTTGTAGTGTTTGTCT
+TAGTGGTTTAGATTCTTTAGACACCTATCCTTCTTTAGAAACTATACAAATTACCATTTCATCTTTTAAA
+TGGGATTTAACTGCTTTTGGCTTAGTTGCAGAGTGGTTTTTGGCATATATTCTTTTCACTAGGTTTTTCT
+ATGTACTTGGATTGGCTGCAATCATGCAATTGTTTTTCAGCTATTTTGCAGTACATTTTATTAGTAATTC
+TTGGCTTATGTGGTTAATAATTAATCTTGTACAAATGGCCCCGATTTCAGCTATGGTTAGAATGTACATC
+TTCTTTGCATCATTTTATTATGTATGGAAAAGTTATGTGCATGTTGTAGACGGTTGTAATTCATCAACTT
+GTATGATGTGTTACAAACGTAATAGAGCAACAAGAGTCGAATGTACAACTATTGTTAATGGTGTTAGAAG
+GTCCTTTTATGTCTATGCTAATGGAGGTAAAGGCTTTTGCAAACTACACAATTGGAATTGTGTTAATTGT
+GATACATTCTGTGCTGGTAGTACATTTATTAGTGATGAAGTTGCGAGAGACTTGTCACTACAGTTTAAAA
+GACCAATAAATCCTACTGACCAGTCTTCTTACATCGTTGATAGTGTTACAGTGAAGAATGGTTCCATCCA
+TCTTTACTTTGATAAAGCTGGTCAAAAGACTTATGAAAGACATTCTCTCTCTCATTTTGTTAACTTAGAC
+AACCTGAGAGCTAATAACACTAAAGGTTCATTGCCTATTAATGTTATAGTTTTTGATGGTAAATCAAAAT
+GTGAAGAATCATCTGCAAAATCAGCGTCTGTTTACTACAGTCAGCTTATGTGTCAACCTATACTGTTACT
+AGATCAGGCATTAGTGTCTGATGTTGGTGATAGTGCGGAAGTTGCAGTTAAAATGTTTGATGCTTACGTT
+AATACGTTTTCATCAACTTTTAACGTACCAATGGAAAAACTCAAAACACTAGTTGCAACTGCAGAAGCTG
+AACTTGCAAAGAATGTGTCCTTAGACAATGTCTTATCTACTTTTA
diff -r 000000000000 -r e7d2c4ed18a5 tool-data/kaiju.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/kaiju.loc.sample Tue Apr 22 14:03:27 2025 +0000
@@ -0,0 +1,5 @@
+# id: db name + date
+# name: what is shown to the user in the select
+# path: of the reference data must contain database.fmi, names.dmp and nodes.dmp
+# version: version used for constructing the DB (or just the current version at the time when pre-computed indices were downloaded)
+#id name path version
\ No newline at end of file
diff -r 000000000000 -r e7d2c4ed18a5 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Tue Apr 22 14:03:27 2025 +0000
@@ -0,0 +1,6 @@
+
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+ value, name, path, version
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+
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diff -r 000000000000 -r e7d2c4ed18a5 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Tue Apr 22 14:03:27 2025 +0000
@@ -0,0 +1,6 @@
+
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+ value, name, path, version
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