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changeset 33:8d01e55c32eb draft

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planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit dfbcd77db9daa30089f3e6262df85a479ac917e1-dirty
author dfornika
date Wed, 07 Mar 2018 14:52:44 -0500
parents c5658160ee70
children 965d2420eebf
files data_managers/data_manager_conf.xml data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.py data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml tools/mentalist_call/mentalist_call.xml
diffstat 7 files changed, 15 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- a/data_managers/data_manager_conf.xml	Fri Jan 26 15:34:45 2018 -0500
+++ b/data_managers/data_manager_conf.xml	Wed Mar 07 14:52:44 2018 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <data_managers>
-  <data_manager tool_file="data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml" id="mentalist_build_db" version="0.1.3">
+  <data_manager tool_file="data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml" id="mentalist_build_db" version="0.1.4">
     <data_table name="mentalist_databases">
       <output>
         <column name="value" />
@@ -15,7 +15,7 @@
       </output>
     </data_table>
   </data_manager>
-  <data_manager tool_file="data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml" id="mentalist_download_cgmlst" version="0.1.3">
+  <data_manager tool_file="data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml" id="mentalist_download_cgmlst" version="0.1.4">
     <data_table name="mentalist_databases">
       <output>
         <column name="value" />
@@ -30,7 +30,7 @@
       </output>
     </data_table>
   </data_manager>
-  <data_manager tool_file="data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml" id="mentalist_download_pubmlst" version="0.1.3">
+  <data_manager tool_file="data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml" id="mentalist_download_pubmlst" version="0.1.4">
     <data_table name="mentalist_databases">
       <output>
         <column name="value" />
@@ -45,7 +45,7 @@
       </output>
     </data_table>
   </data_manager>
-  <data_manager tool_file="data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml" id="mentalist_download_enterobase" version="0.1.3">
+  <data_manager tool_file="data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml" id="mentalist_download_enterobase" version="0.1.4">
     <data_table name="mentalist_databases">
       <output>
         <column name="value" />
--- a/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml	Fri Jan 26 15:34:45 2018 -0500
+++ b/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml	Wed Mar 07 14:52:44 2018 -0500
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
-<tool id="mentalist_build_db" name="MentaLiST Build DB" tool_type="manage_data" version="0.1.3">
+<tool id="mentalist_build_db" name="MentaLiST Build DB" tool_type="manage_data" version="0.1.4">
   <requirements>
-    <requirement type="package" version="0.1.3">mentalist</requirement>
+    <requirement type="package" version="0.1.4">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
   <![CDATA[
--- a/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml	Fri Jan 26 15:34:45 2018 -0500
+++ b/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml	Wed Mar 07 14:52:44 2018 -0500
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
-<tool id="mentalist_download_cgmlst" name="MentaLiST Download from cgMLST" tool_type="manage_data" version="0.1.3">
+<tool id="mentalist_download_cgmlst" name="MentaLiST Download from cgMLST" tool_type="manage_data" version="0.1.4">
   <requirements>
-    <requirement type="package" version="0.1.3">mentalist</requirement>
+    <requirement type="package" version="0.1.4">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
     <![CDATA[
--- a/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.py	Fri Jan 26 15:34:45 2018 -0500
+++ b/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.py	Wed Mar 07 14:52:44 2018 -0500
@@ -30,7 +30,7 @@
     if return_code:
         print("Error building database.", file=sys.stderr)
         sys.exit( return_code )
-    data_table_entry = dict( value=database_path, dbkey='PubMLST', name=display_name, path=database_name )
+    data_table_entry = dict( value=database_path, dbkey='Enterobase', name=display_name, path=database_name )
     for data_table_name in data_table_names:
         _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
 
--- a/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml	Fri Jan 26 15:34:45 2018 -0500
+++ b/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml	Wed Mar 07 14:52:44 2018 -0500
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
-<tool id="mentalist_download_enterobase" name="MentaLiST Download from Enterobase" tool_type="manage_data" version="0.1.3">
+<tool id="mentalist_download_enterobase" name="MentaLiST Download from Enterobase" tool_type="manage_data" version="0.1.4">
   <requirements>
-    <requirement type="package" version="0.1.3">mentalist</requirement>
+    <requirement type="package" version="0.1.4">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
     <![CDATA[
--- a/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml	Fri Jan 26 15:34:45 2018 -0500
+++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml	Wed Mar 07 14:52:44 2018 -0500
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
-<tool id="mentalist_download_pubmlst" name="MentaLiST Download from pubMLST" tool_type="manage_data" version="0.1.3">
+<tool id="mentalist_download_pubmlst" name="MentaLiST Download from pubMLST" tool_type="manage_data" version="0.1.4">
   <requirements>
-    <requirement type="package" version="0.1.3">mentalist</requirement>
+    <requirement type="package" version="0.1.4">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
     <![CDATA[
--- a/tools/mentalist_call/mentalist_call.xml	Fri Jan 26 15:34:45 2018 -0500
+++ b/tools/mentalist_call/mentalist_call.xml	Wed Mar 07 14:52:44 2018 -0500
@@ -1,6 +1,6 @@
-<tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.1.3">
+<tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.1.4">
   <requirements>
-    <requirement type="package" version="0.1.3">mentalist</requirement>
+    <requirement type="package" version="0.1.4">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
     mentalist