# HG changeset patch
# User iuc
# Date 1575460268 18000
# Node ID 9a5be5b1a5c912af902aa28297aa4e404f3f7103
# Parent  9bdcba262627581b4b1662d3a8b8bea214c22197
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"

diff -r 9bdcba262627 -r 9a5be5b1a5c9 kraken-translate.xml
--- a/kraken-translate.xml	Mon Aug 07 17:29:45 2017 -0400
+++ b/kraken-translate.xml	Wed Dec 04 06:51:08 2019 -0500
@@ -27,10 +27,10 @@
     </outputs>
     <tests>
         <test>
-            <param name="input" value="kraken_translate_test1.tab" ftype="tabular"/>
+            <param name="input" value="kraken-translate/kraken_translate_test1.tab" ftype="tabular"/>
             <param name="mpa-format" value="false"/>
-            <param name="kraken_database" value="test_db"/>
-            <output name="translated" file="kraken_translate_test1_output.tab" ftype="tabular"/>
+            <param name="kraken_database" value="new_style_test_entry"/>
+            <output name="translated" file="kraken-translate/kraken_translate_test1_output.tab" ftype="tabular"/>
         </test>
     </tests>
     <help><![CDATA[
diff -r 9bdcba262627 -r 9a5be5b1a5c9 macros.xml
--- a/macros.xml	Mon Aug 07 17:29:45 2017 -0400
+++ b/macros.xml	Wed Dec 04 06:51:08 2019 -0500
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@WRAPPER_VERSION@">1.2.3</token>
+    <token name="@WRAPPER_VERSION@">1.3.1</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="0.10.6_eaf8fb68">kraken</requirement>
+            <requirement type="package" version="1.1.1">kraken</requirement>
         </requirements>
     </xml>
     <xml name="version_command">
@@ -23,6 +23,10 @@
             <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
         </citations>
     </xml>
-    <token name="@INPUT_DATABASE@">--db ${kraken_database.fields.name}</token>
-    <token name="@SET_DATABASE_PATH@">export KRAKEN_DB_PATH="${kraken_database.fields.path}"</token>
+    <!-- See the kraken_databases.loc.sample documentation,
+         this if statement is for backward compatibility as early
+         versions of the wrapper assumed the UI facing field name
+         was also part of the directory path -->
+    <token name="@SET_DATABASE_PATH@">if [ -d '${kraken_database.fields.path}/${kraken_database.fields.name}' ]; then export KRAKEN_DEFAULT_DB='${kraken_database.fields.path}/${kraken_database.fields.name}'; else export KRAKEN_DEFAULT_DB='${kraken_database.fields.path}'; fi</token>
+    <token name="@INPUT_DATABASE@">--db "\$KRAKEN_DEFAULT_DB"</token>
 </macros>
diff -r 9bdcba262627 -r 9a5be5b1a5c9 test-data/kraken-translate/kraken_translate_test1.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kraken-translate/kraken_translate_test1.tab	Wed Dec 04 06:51:08 2019 -0500
@@ -0,0 +1,4 @@
+C	gi|145231|gb|M33724.1|ECOALPHOA	83333	171	83333:162
+C	gi|145232|gb|M33725.1|ECOALPHOB	83333	183	83333:174
+C	gi|145234|gb|M33727.1|ECOALPHOE	83333	97	83333:88
+C	gi|146195|gb|J01619.1|ECOGLTA	83333	3850	83333:3841
diff -r 9bdcba262627 -r 9a5be5b1a5c9 test-data/kraken-translate/kraken_translate_test1_output.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kraken-translate/kraken_translate_test1_output.tab	Wed Dec 04 06:51:08 2019 -0500
@@ -0,0 +1,4 @@
+gi|145231|gb|M33724.1|ECOALPHOA	root;cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli;Escherichia coli K-12
+gi|145232|gb|M33725.1|ECOALPHOB	root;cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli;Escherichia coli K-12
+gi|145234|gb|M33727.1|ECOALPHOE	root;cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli;Escherichia coli K-12
+gi|146195|gb|J01619.1|ECOGLTA	root;cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli;Escherichia coli K-12
diff -r 9bdcba262627 -r 9a5be5b1a5c9 test-data/kraken-translate/test_database.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kraken-translate/test_database.loc	Wed Dec 04 06:51:08 2019 -0500
@@ -0,0 +1,20 @@
+# Tab separated with three columns:
+# - value (Galaxy records this in the Galaxy DB)
+# - name (Galaxy shows this in the UI)
+# - path (folder name containing the Kraken DB)
+#
+# Modern usage assumes $path is the folder containing
+# the Kraken database of interest:
+#
+new_style_test_entry	"Test Database"	${__HERE__}/test_db
+
+# The kraken wrapper still supports an alternative
+# legacy usage where $path/$name is the folder
+# containing the Kraken database of interest, meaning
+# $name must be both a folder name and human readable
+# description of the DB to show in the Galaxy UI:
+old_style_test_entry	test_db	${__HERE__}
+
+# NOTE: This legacy style should be avoided as other
+# tools also using the kraken_database.loc file may
+# not understand it!
diff -r 9bdcba262627 -r 9a5be5b1a5c9 test-data/kraken_translate_test1.tab
--- a/test-data/kraken_translate_test1.tab	Mon Aug 07 17:29:45 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-C	gi|145231|gb|M33724.1|ECOALPHOA	83333	171	83333:162
-C	gi|145232|gb|M33725.1|ECOALPHOB	83333	183	83333:174
-C	gi|145234|gb|M33727.1|ECOALPHOE	83333	97	83333:88
-C	gi|146195|gb|J01619.1|ECOGLTA	83333	3850	83333:3841
diff -r 9bdcba262627 -r 9a5be5b1a5c9 test-data/kraken_translate_test1_output.tab
--- a/test-data/kraken_translate_test1_output.tab	Mon Aug 07 17:29:45 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-gi|145231|gb|M33724.1|ECOALPHOA	root;cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli;Escherichia coli K-12
-gi|145232|gb|M33725.1|ECOALPHOB	root;cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli;Escherichia coli K-12
-gi|145234|gb|M33727.1|ECOALPHOE	root;cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli;Escherichia coli K-12
-gi|146195|gb|J01619.1|ECOGLTA	root;cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli;Escherichia coli K-12
diff -r 9bdcba262627 -r 9a5be5b1a5c9 test-data/test_database.loc
--- a/test-data/test_database.loc	Mon Aug 07 17:29:45 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-test_db	test_db	${__HERE__}
\ No newline at end of file
diff -r 9bdcba262627 -r 9a5be5b1a5c9 test-data/test_db/database.idx
Binary file test-data/test_db/database.idx has changed
diff -r 9bdcba262627 -r 9a5be5b1a5c9 test-data/test_db/database.kdb
Binary file test-data/test_db/database.kdb has changed
diff -r 9bdcba262627 -r 9a5be5b1a5c9 test-data/test_db/taxonomy/names.dmp
--- a/test-data/test_db/taxonomy/names.dmp	Mon Aug 07 17:29:45 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,74 +0,0 @@
-83333	|	Escherichia coli K-12	|		|	scientific name	|
-83333	|	Escherichia coli K12	|		|	equivalent name	|
-562	|	"Bacillus coli" Migula 1895	|		|	authority	|
-562	|	"Bacterium coli commune" Escherich 1885	|		|	authority	|
-562	|	"Bacterium coli" (Migula 1895) Lehmann and Neumann 1896	|		|	authority	|
-562	|	ATCC 11775	|		|	type material	|
-562	|	Bacillus coli	|		|	synonym	|
-562	|	Bacterium coli	|		|	synonym	|
-562	|	Bacterium coli commune	|		|	synonym	|
-562	|	CCUG 24	|		|	type material	|
-562	|	CCUG 29300	|		|	type material	|
-562	|	CIP 54.8	|		|	type material	|
-562	|	DSM 30083	|		|	type material	|
-562	|	Enterococcus coli	|		|	synonym	|
-562	|	Escherchia coli	|		|	misspelling	|
-562	|	Escherichia coli	|		|	scientific name	|
-562	|	Escherichia coli (Migula 1895) Castellani and Chalmers 1919	|		|	authority	|
-562	|	Escherichia sp. MAR	|		|	includes	|
-562	|	Escherichia/Shigella coli	|		|	equivalent name	|
-562	|	Eschericia coli	|		|	misspelling	|
-562	|	JCM 1649	|		|	type material	|
-562	|	LMG 2092	|		|	type material	|
-562	|	NBRC 102203	|		|	type material	|
-562	|	NCCB 54008	|		|	type material	|
-562	|	NCTC 9001	|		|	type material	|
-562	|	bacterium 10a	|		|	includes	|
-562	|	bacterium E3	|		|	includes	|
-561	|	Escherchia	|		|	misspelling	|
-561	|	Escherichia	|		|	scientific name	|
-561	|	Escherichia Castellani and Chalmers 1919	|		|	authority	|
-543	|	Enterobacteraceae	|		|	synonym	|
-543	|	Enterobacteraceae (ex Lapage 1979) Lapage 1982, fam. nov., nom. rev.	|		|	synonym	|
-543	|	Enterobacteriaceae	|		|	scientific name	|
-543	|	Enterobacteriaceae (ex Rahn 1937) Ewing et al. 1980, fam. nov., nom. rev.	|		|	synonym	|
-543	|	Enterobacteriaceae Rahn 1937	|		|	synonym	|
-543	|	gamma-3 proteobacteria	|	gamma-3 proteobacteria <#1>	|	in-part	|
-91347	|	'Enterobacteriales'	|		|	synonym	|
-91347	|	Enterobacteriaceae and related endosymbionts	|		|	synonym	|
-91347	|	Enterobacteriaceae group	|		|	synonym	|
-91347	|	Enterobacteriales	|		|	scientific name	|
-91347	|	enterobacteria	|	enterobacteria<blast91347>	|	blast name	|
-91347	|	gamma-3 proteobacteria	|	gamma-3 proteobacteria <#5>	|	in-part	|
-1236	|	Gammaproteobacteria	|		|	scientific name	|
-1236	|	Gammaproteobacteria Garrity et al. 2005	|		|	synonym	|
-1236	|	Proteobacteria gamma subdivision	|		|	synonym	|
-1236	|	Purple bacteria, gamma subdivision	|		|	synonym	|
-1236	|	g-proteobacteria	|	gamma proteos<blast1236>	|	blast name	|
-1236	|	gamma proteobacteria	|		|	synonym	|
-1236	|	gamma subdivision	|		|	synonym	|
-1236	|	gamma subgroup	|		|	synonym	|
-1224	|	Proteobacteria	|		|	scientific name	|
-1224	|	Proteobacteria Garrity et al. 2005	|		|	authority	|
-1224	|	Proteobacteria [class] Stackebrandt et al. 1988	|		|	authority	|
-1224	|	not Proteobacteria Cavalier-Smith 2002	|		|	authority	|
-1224	|	proteobacteria	|	proteobacteria<blast1224>	|	blast name	|
-1224	|	purple bacteria	|		|	common name	|
-1224	|	purple bacteria and relatives	|		|	common name	|
-1224	|	purple non-sulfur bacteria	|		|	common name	|
-1224	|	purple photosynthetic bacteria	|		|	common name	|
-1224	|	purple photosynthetic bacteria and relatives	|		|	common name	|
-2	|	Bacteria	|	Bacteria <prokaryote>	|	scientific name	|
-2	|	Monera	|	Monera <Bacteria>	|	in-part	|
-2	|	Procaryotae	|	Procaryotae <Bacteria>	|	in-part	|
-2	|	Prokaryota	|	Prokaryota <Bacteria>	|	in-part	|
-2	|	Prokaryotae	|	Prokaryotae <Bacteria>	|	in-part	|
-2	|	bacteria	|	bacteria <blast2>	|	blast name	|
-2	|	eubacteria	|		|	genbank common name	|
-2	|	not Bacteria Haeckel 1894	|		|	synonym	|
-2	|	prokaryote	|	prokaryote <Bacteria>	|	in-part	|
-2	|	prokaryotes	|	prokaryotes <Bacteria>	|	in-part	|
-1	|	all	|		|	synonym	|
-1	|	root	|		|	scientific name	|
-131567	|	biota	|		|	synonym	|
-131567	|	cellular organisms	|		|	scientific name	|
diff -r 9bdcba262627 -r 9a5be5b1a5c9 test-data/test_db/taxonomy/nodes.dmp
--- a/test-data/test_db/taxonomy/nodes.dmp	Mon Aug 07 17:29:45 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-83333	|	562	|	no rank	|		|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
-562	|	561	|	species	|	EC	|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
-561	|	543	|	genus	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
-543	|	91347	|	family	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
-91347	|	1236	|	order	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
-1236	|	1224	|	class	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
-1224	|	2	|	phylum	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
-2	|	131567	|	superkingdom	|		|	0	|	0	|	11	|	0	|	0	|	0	|	0	|	0	|		|
-131567	|	1	|	no rank	|		|	8	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
-1	|	1	|	no rank	|		|	8	|	0	|	1	|	0	|	0	|	0	|	0	|	0	|		|
diff -r 9bdcba262627 -r 9a5be5b1a5c9 tool-data/kraken_databases.loc.sample
--- a/tool-data/kraken_databases.loc.sample	Mon Aug 07 17:29:45 2017 -0400
+++ b/tool-data/kraken_databases.loc.sample	Wed Dec 04 06:51:08 2019 -0500
@@ -0,0 +1,18 @@
+# Expect three columns, tab separated, as follows:
+# - value (Galaxy records this in the Galaxy DB)
+# - name (Galaxy shows this in the UI)
+# - path (folder name containing the Kraken DB)
+#
+# e.g.
+# plants2018<tab>Plant genomes (2018)<tab>/path/to/krakenDB/plants_2018
+#
+# For backward compatibility the Kraken wrapper also accepts:
+# - value (Galaxy records this in the Galaxy DB)
+# - name (Final part of folder name, Galaxy shows this in the UI)
+# - path (Parent folder name, where $path/$name contains the Kraken DB)
+#
+# e.g.
+# plants2018<tab>plants_2018<tab>/path/to/krakenDB
+#
+# Please avoid this legacy usage, as not all tools using
+# the kraken_databases.loc file will understand it.