# HG changeset patch
# User iuc
# Date 1723658471 0
# Node ID b6dd55c620f8bb56795199d793b94828a2f21549
# Parent  0fd79958fac67dbaddac5febfc482a59a0929ebf
planemo upload for repository https://github.com/shenwei356/taxonkit commit 703018a5f716e73f2bace7fffee12ae4329fb2c2

diff -r 0fd79958fac6 -r b6dd55c620f8 macros.xml
--- 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>
diff -r 0fd79958fac6 -r b6dd55c620f8 test-data/name2taxid_result1.tsv
--- /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	
diff -r 0fd79958fac6 -r b6dd55c620f8 test-data/name2taxid_result2.tsv
--- /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	
diff -r 0fd79958fac6 -r b6dd55c620f8 test-data/name2taxid_result3.tsv
--- /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
diff -r 0fd79958fac6 -r b6dd55c620f8 test-data/name2taxid_test1.tsv
--- /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
diff -r 0fd79958fac6 -r b6dd55c620f8 test-data/name2taxid_test2.tsv
--- /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
diff -r 0fd79958fac6 -r b6dd55c620f8 test-data/name2taxid_test3.txt
--- /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
diff -r 0fd79958fac6 -r b6dd55c620f8 test-data/ncbi_taxonomy.loc.test
--- 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
diff -r 0fd79958fac6 -r b6dd55c620f8 test-data/test-db/delnodes.dmp
--- 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
diff -r 0fd79958fac6 -r b6dd55c620f8 test-data/test-db/names.dmp
--- 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	|
diff -r 0fd79958fac6 -r b6dd55c620f8 test-data/test.tar.gz
Binary file test-data/test.tar.gz has changed
diff -r 0fd79958fac6 -r b6dd55c620f8 tool-data/ncbi_taxonomy.loc.sample
--- 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"  ${__HERE__}/test-db
diff -r 0fd79958fac6 -r b6dd55c620f8 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Fri Jul 26 09:26:02 2024 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Aug 14 18:01:11 2024 +0000
@@ -3,6 +3,6 @@
         <!-- Locations of taxonomy data downloaded from NCBI -->
     <table name="ncbi_taxonomy" comment_char="#">
         <columns>value, name, path</columns>
-        <file path="tool-data/ncbi_taxonomy.loc" />
+        <file path="${__HERE__}/test-data/ncbi_taxonomy.loc.test" />
     </table>
 </tables>