Mercurial > repos > devteam > kraken_translate

changeset 1:475284b74179 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 3abfc7eb2999fa588862b84c453012c811fa8350
author devteam
date Mon, 21 Mar 2016 12:07:33 -0400
parents 77ca66b1f5e9
children b9971bca4b01
files kraken-translate.xml macros.xml test-data/kraken_translate_test1.tab test-data/kraken_translate_test1_output.tab test-data/test_database.loc test-data/test_db/database.idx test-data/test_db/database.kdb test-data/test_db/taxonomy/names.dmp test-data/test_db/taxonomy/nodes.dmp tool_data_table_conf.xml.test tool_dependencies.xml
diffstat 11 files changed, 119 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/kraken-translate.xml	Thu Jul 23 10:56:31 2015 -0400
+++ b/kraken-translate.xml	Mon Mar 21 12:07:33 2016 -0400
@@ -1,10 +1,13 @@
-<tool id="kraken-translate" name="Kraken-translate" version="1.1.0">
+<tool id="kraken-translate" name="Kraken-translate" version="1.2.0">
     <description>
         convert taxonomy IDs to names
     </description>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
     <command>
         <![CDATA[
         @SET_DATABASE_PATH@ &&
@@ -19,6 +22,14 @@
     <outputs>
         <data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />
     </outputs>
+    <tests>
+        <test>
+            <param name="input" value="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"/>
+        </test>
+    </tests>
     <help>
         <![CDATA[
 
@@ -45,8 +56,5 @@
 Taxonomy assignments above the superkingdom rank are represented as just "root" when using the ``--mpa-report`` option with kraken-translate.
         ]]>
     </help>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
-    <expand macro="version_command" />
     <expand macro="citations" />
 </tool>
--- a/macros.xml	Thu Jul 23 10:56:31 2015 -0400
+++ b/macros.xml	Mon Mar 21 12:07:33 2016 -0400
@@ -2,7 +2,10 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="0.10.5">kraken</requirement>
+            <requirement type="package" version="0.10.6_eaf8fb68">kraken</requirement>
+        </requirements>
+        <requirements>
+            <requirement type="package" version="0.10.6-eaf8fb68">kraken</requirement>
         </requirements>
     </xml>
     <xml name="stdio">
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kraken_translate_test1.tab	Mon Mar 21 12:07:33 2016 -0400
@@ -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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kraken_translate_test1_output.tab	Mon Mar 21 12:07:33 2016 -0400
@@ -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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_database.loc	Mon Mar 21 12:07:33 2016 -0400
@@ -0,0 +1,1 @@
+test_db	test_db	${__HERE__}
\ No newline at end of file
Binary file test-data/test_db/database.idx has changed
Binary file test-data/test_db/database.kdb has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_db/taxonomy/names.dmp	Mon Mar 21 12:07:33 2016 -0400
@@ -0,0 +1,74 @@
+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	|
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_db/taxonomy/nodes.dmp	Mon Mar 21 12:07:33 2016 -0400
@@ -0,0 +1,10 @@
+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	|		|
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Mon Mar 21 12:07:33 2016 -0400
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<tables>
+    <!-- Locations of Kraken database in the required format -->
+    <table name="kraken_databases" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/test_database.loc" />
+    </table>
+</tables>
--- a/tool_dependencies.xml	Thu Jul 23 10:56:31 2015 -0400
+++ b/tool_dependencies.xml	Mon Mar 21 12:07:33 2016 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="kraken" version="0.10.5">
-      <repository changeset_revision="89a36b0f718c" name="package_kraken_0_10_5" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+  <package name="kraken" version="0.10.6-eaf8fb68">
+      <repository changeset_revision="0743afe4dcb8" name="package_kraken_0_10_6_eaf8fb68" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>