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changeset 2:a671367c326e draft

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"planemo upload for repository https://github.com/arpcard/rgi commit 481838067117d0c8ae84bc92ee58f47cfc18aa5f"
author card
date Tue, 17 Nov 2020 00:23:36 +0000
parents f96cbb663aa9
children bfbfc24c5af2
files data_managers/data_manager_conf.xml data_managers/data_manager_rgi_build_db/data_manager/rgi_database_builder.xml data_managers/data_manager_rgi_build_db/tool_data_table_conf.xml.sample rgi.xml
diffstat 4 files changed, 8 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/data_managers/data_manager_conf.xml	Fri Feb 28 13:38:11 2020 -0500
+++ b/data_managers/data_manager_conf.xml	Tue Nov 17 00:23:36 2020 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <data_managers>
-    <data_manager tool_file="data_manager_rgi_build_db/data_manager/rgi_database_builder.xml" id="rgi_database_builder" version="1.0.0">
+    <data_manager tool_file="data_manager_rgi_build_db/data_manager/rgi_database_builder.xml" id="rgi_database_builder" version="1.1.0">
         <!-- Defines a Data Table to be modified -->
         <data_table name="rgi_databases">
             <!-- Handle the output of the Data Manager Tool -->
--- a/data_managers/data_manager_rgi_build_db/data_manager/rgi_database_builder.xml	Fri Feb 28 13:38:11 2020 -0500
+++ b/data_managers/data_manager_rgi_build_db/data_manager/rgi_database_builder.xml	Tue Nov 17 00:23:36 2020 +0000
@@ -1,15 +1,15 @@
 <?xml version="1.0"?>
-<tool id="rgi_database_builder" name="RGI Database Builder" tool_type="manage_data" version="1.0.0">
+<tool id="rgi_database_builder" name="RGI Database Builder" tool_type="manage_data" version="1.1.0">
     <description>Download and build the CARD database for RGI</description>
     <requirements>
-	<requirement type="package" version="5.1.0">rgi</requirement>
+	<requirement type="package" version="5.1.1">rgi</requirement>
     </requirements>
     <stdio>
         <exit_code description="Error" level="fatal" range="1:" />
     </stdio>
-    <command interpreter="python3">
+    <command>
     <![CDATA[
-        rgi_database_builder.py --out "${out_file}"
+        python3 rgi_database_builder.py --out "${out_file}"
         #if $name:
             --name "${name}"
         #end if
--- a/data_managers/data_manager_rgi_build_db/tool_data_table_conf.xml.sample	Fri Feb 28 13:38:11 2020 -0500
+++ b/data_managers/data_manager_rgi_build_db/tool_data_table_conf.xml.sample	Tue Nov 17 00:23:36 2020 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tables>
     <!-- Locations of RGI database in the required format -->
-    <table name="rgi_databases" comment_char="#">
+    <table name="rgi_databases" comment_char="#" allow_duplicate_entries="False">
         <columns>value, name, path</columns>
         <file path="tool-data/rgi_databases.loc" />
     </table>
--- a/rgi.xml	Fri Feb 28 13:38:11 2020 -0500
+++ b/rgi.xml	Tue Nov 17 00:23:36 2020 +0000
@@ -1,7 +1,7 @@
-<tool id="rgi" name="Resistance Gene Identifier (RGI)" version="5.1.0">
+<tool id="rgi" name="Resistance Gene Identifier (RGI)" version="5.1.1">
     <description>This tool predicts resistome(s) from protein or nucleotide data based on homology and SNP models.</description>
     <requirements>
-        <requirement type="package" version="5.1.0">rgi</requirement>
+        <requirement type="package" version="5.1.1">rgi</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />