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changeset 3:6e9aea89e388 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 962161e1dde26559d0bc1ce5d7b75d2f354606c5
author iuc
date Mon, 04 Sep 2017 02:47:12 -0400
parents 2aa02d2a6af3
children 78c75f134c16
files abricate.xml abricate_list.xml test-data/output_db-card.txt test-data/output_list.txt
diffstat 4 files changed, 14 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- a/abricate.xml	Tue Jul 18 13:56:16 2017 -0400
+++ b/abricate.xml	Mon Sep 04 02:47:12 2017 -0400
@@ -1,6 +1,6 @@
-<tool id="abricate" name="ABRicate" version="0.5">
+<tool id="abricate" name="ABRicate" version="0.7">
     <requirements>
-        <requirement type="package" version="0.5">abricate</requirement>
+        <requirement type="package" version="0.7">abricate</requirement>
     </requirements>
 
     <version_command>abricate --version</version_command>
--- a/abricate_list.xml	Tue Jul 18 13:56:16 2017 -0400
+++ b/abricate_list.xml	Mon Sep 04 02:47:12 2017 -0400
@@ -1,12 +1,12 @@
-<tool id="abricate_list" name="ABRicate List" version="0.5">
+<tool id="abricate_list" name="ABRicate List" version="0.7">
     <requirements>
-        <requirement type="package" version="0.5">abricate</requirement>
+        <requirement type="package" version="0.7">abricate</requirement>
     </requirements>
 
     <version_command>abricate --version</version_command>
 
     <command detect_errors="exit_code"><![CDATA[
-        abricate --list 2> '$report'
+        abricate --list > '$report'
     ]]></command>
 
     <inputs>
@@ -18,7 +18,7 @@
 
     <tests>
         <test>
-            <output name="report" ftype="txt" file="output_list.txt" compare="contains"/>
+            <output name="report" ftype="txt" file="output_list.txt" compare="contains" />
         </test>
     </tests>
 
--- a/test-data/output_db-card.txt	Tue Jul 18 13:56:16 2017 -0400
+++ b/test-data/output_db-card.txt	Mon Sep 04 02:47:12 2017 -0400
@@ -14,4 +14,3 @@
 NC_002952.2	1796513	1797245	ErmA	1-733/733	===============	0/0	100.00	100.00	card	NC_009632:49745-50477
 NC_002952.2	1913826	1914672	PC1_beta-lactamase_(blaZ)	1-847/847	===============	0/0	100.00	97.17	card	NC_010066:9683-10529
 NC_002952.2	2047036	2048773	sav1866	1-1738/1738	===============	0/0	100.00	99.19	card	NC_002951:1987720-1989457
-NC_002952.2	2488459	2488878	FosB	1-420/420	===============	0/0	100.00	79.05	card	NC_010419.1:17043-17463
--- a/test-data/output_list.txt	Tue Jul 18 13:56:16 2017 -0400
+++ b/test-data/output_list.txt	Mon Sep 04 02:47:12 2017 -0400
@@ -1,7 +1,8 @@
-abricate: corrupt database? - 
-argannot:  1749 sequences -  Jul 8, 2017
-card:  2124 sequences -  Jul 8, 2017
-ncbibetalactamase:  1557 sequences -  Mar 17, 2017
-plasmidfinder:  263 sequences -  Mar 19, 2017
-resfinder:  2228 sequences -  Jul 8, 2017
-vfdb:  2597 sequences -  Mar 17, 2017
+DATABASE	SEQUENCES	DATE
+argannot	1749	
+card	2153	
+ncbi	4124	
+ncbibetalactamase	1557	
+plasmidfinder	263	
+resfinder	2228	
+vfdb	2597