Mercurial > repos > iuc > profile2cami
changeset 1:b6dd55c620f8 draft
planemo upload for repository https://github.com/shenwei356/taxonkit commit 703018a5f716e73f2bace7fffee12ae4329fb2c2
| author | iuc |
|---|---|
| date | Wed, 14 Aug 2024 18:01:11 +0000 |
| parents | 0fd79958fac6 |
| children | edc9559928d3 |
| files | macros.xml test-data/name2taxid_result1.tsv test-data/name2taxid_result2.tsv test-data/name2taxid_result3.tsv test-data/name2taxid_test1.tsv test-data/name2taxid_test2.tsv test-data/name2taxid_test3.txt test-data/ncbi_taxonomy.loc.test test-data/test-db/delnodes.dmp test-data/test-db/names.dmp test-data/test.tar.gz tool-data/ncbi_taxonomy.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 13 files changed, 57 insertions(+), 5 deletions(-) [+] |
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--- a/macros.xml Fri Jul 26 09:26:02 2024 +0000 +++ b/macros.xml Wed Aug 14 18:01:11 2024 +0000 @@ -1,4 +1,4 @@ - <macros> +<macros> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">taxonkit</requirement>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/name2taxid_result1.tsv Wed Aug 14 18:01:11 2024 +0000 @@ -0,0 +1,5 @@ +Homo sapiens 9606 +Akkermansia muciniphila ATCC BAA-835 349741 +Akkermansia muciniphila 239935 +Mouse Intracisternal A-particle 11932 +Enterococcus coli
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/name2taxid_result2.tsv Wed Aug 14 18:01:11 2024 +0000 @@ -0,0 +1,4 @@ +test Homo sapiens 9606 +test Akkermansia muciniphila ATCC BAA-835 349741 +test Akkermansia muciniphila 239935 +test Mouse Intracisternal A-particle 11932
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/name2taxid_result3.tsv Wed Aug 14 18:01:11 2024 +0000 @@ -0,0 +1,4 @@ +Drosophila 7215 +Drosophila 32281 +Drosophila 2081351 +Enterococcus coli 562
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/name2taxid_test1.tsv Wed Aug 14 18:01:11 2024 +0000 @@ -0,0 +1,5 @@ +Homo sapiens +Akkermansia muciniphila ATCC BAA-835 +Akkermansia muciniphila +Mouse Intracisternal A-particle +Enterococcus coli \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/name2taxid_test2.tsv Wed Aug 14 18:01:11 2024 +0000 @@ -0,0 +1,4 @@ +test Homo sapiens +test Akkermansia muciniphila ATCC BAA-835 +test Akkermansia muciniphila +test Mouse Intracisternal A-particle \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/name2taxid_test3.txt Wed Aug 14 18:01:11 2024 +0000 @@ -0,0 +1,2 @@ +Drosophila +Enterococcus coli \ No newline at end of file
--- a/test-data/ncbi_taxonomy.loc.test Fri Jul 26 09:26:02 2024 +0000 +++ b/test-data/ncbi_taxonomy.loc.test Wed Aug 14 18:01:11 2024 +0000 @@ -1,1 +1,2 @@ +#value name path test-db-tox Test Database ${__HERE__}/test-db \ No newline at end of file
--- a/test-data/test-db/delnodes.dmp Fri Jul 26 09:26:02 2024 +0000 +++ b/test-data/test-db/delnodes.dmp Wed Aug 14 18:01:11 2024 +0000 @@ -14997,4 +14997,4 @@ 2900873 | 2900872 | 2900871 | -2900870 | +2900870 | \ No newline at end of file
--- a/test-data/test-db/names.dmp Fri Jul 26 09:26:02 2024 +0000 +++ b/test-data/test-db/names.dmp Wed Aug 14 18:01:11 2024 +0000 @@ -72,4 +72,31 @@ 1 | root | | scientific name | 131567 | biota | | synonym | 131567 | cellular organisms | | scientific name | - +7215 | Drosophila | Drosophila <flies,genus> | scientific name | +7215 | Drosophila Fallen, 1823 | | authority | +7215 | fruit flies | fruit flies <Drosophila> | genbank common name | +7215 | fruit fly | fruit fly <Drosophila> | common name | +32281 | Drosophila (Drosophila) Fallen, 1823 | | authority | +32281 | Drosophila | Drosophila <flies,subgenus> | scientific name | +32281 | Drosophila (Drosophila) | | includes | +9606 | Homo sapiens Linnaeus, 1758 | | authority | +9606 | Homo sapiens | | scientific name | +9606 | human | | genbank common name | +349741 | Akkermansia muciniphila ATCC BAA-835 | | scientific name | +349741 | Akkermansia muciniphila Muc | | synonym | +349741 | Akkermansia muciniphila strain ATCC BAA-835 | | equivalent name | +349741 | Akkermansia muciniphila str. ATCC BAA-835 | | equivalent name | +349741 | Akkermansia sp. Muc | | synonym | +239935 | Akkermansia muciniphila Derrien et al. 2004 emend. Hahnke et al. 2016 | | authority | +239935 | Akkermansia muciniphila | | scientific name | +239935 | Akkermansia sp. YL44 | | includes | +239935 | ATCC BAA-835 | ATCC BAA-835 <type strain> | type material | +239935 | CIP 107961 | CIP 107961 <type strain> | type material | +239935 | culture-collection:ATCC:BAA:835 | culture-collection:ATCC:BAA:835 <type strain> | type material | +239935 | DSM 22959 | DSM 22959 <type strain> | type material | +239935 | strain Muc | strain Muc <type strain> | type material | +11932 | Mouse Intracisternal A-particle (IAP-MIAE) | | equivalent name | +11932 | Mouse intracisternal A-particle MIAE | | equivalent name | +11932 | Mouse Intracisternal A-particle | | scientific name | +2081351 | Drosophila | Drosophila <basidiomycete fungi> | scientific name | +2081351 | Drosophila Quel., 1886 | | authority |
--- a/tool-data/ncbi_taxonomy.loc.sample Fri Jul 26 09:26:02 2024 +0000 +++ b/tool-data/ncbi_taxonomy.loc.sample Wed Aug 14 18:01:11 2024 +0000 @@ -1,2 +1,2 @@ #value name path -# test-db-tox "Test Database" tool-data/test-db \ No newline at end of file +test-db-tox "Test Database" ${__HERE__}/test-db
--- a/tool_data_table_conf.xml.sample Fri Jul 26 09:26:02 2024 +0000 +++ b/tool_data_table_conf.xml.sample Wed Aug 14 18:01:11 2024 +0000 @@ -3,6 +3,6 @@ <!-- Locations of taxonomy data downloaded from NCBI --> <table name="ncbi_taxonomy" comment_char="#"> <columns>value, name, path</columns> - <file path="tool-data/ncbi_taxonomy.loc" /> + <file path="${__HERE__}/test-data/ncbi_taxonomy.loc.test" /> </table> </tables>