# HG changeset patch
# User dfornika
# Date 1521069821 14400
# Node ID 965d2420eebfa017f8fd8abd31d4fdd711071cf5
# Parent  8d01e55c32eb0a45786e49ada7ddc91f1b02b34d
planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 20b8767aa2b376a67c5f7106c56757f14b055c2c-dirty

diff -r 8d01e55c32eb -r 965d2420eebf data_managers/data_manager_conf.xml
--- a/data_managers/data_manager_conf.xml	Wed Mar 07 14:52:44 2018 -0500
+++ b/data_managers/data_manager_conf.xml	Wed Mar 14 19:23:41 2018 -0400
@@ -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="0.1.4">
+  <data_manager tool_file="data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml" id="mentalist_build_db" version="0.1.3">
     <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="0.1.4">
+  <data_manager tool_file="data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml" id="mentalist_download_cgmlst" version="0.1.3">
     <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="0.1.4">
+  <data_manager tool_file="data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml" id="mentalist_download_pubmlst" version="0.1.3">
     <data_table name="mentalist_databases">
       <output>
         <column name="value" />
diff -r 8d01e55c32eb -r 965d2420eebf data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml
--- a/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml	Wed Mar 07 14:52:44 2018 -0500
+++ b/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml	Wed Mar 14 19:23:41 2018 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
-<tool id="mentalist_build_db" name="MentaLiST Build DB" tool_type="manage_data" version="0.1.4">
+<tool id="mentalist_build_db" name="MentaLiST Build DB" tool_type="manage_data" version="0.2.1">
   <requirements>
-    <requirement type="package" version="0.1.4">mentalist</requirement>
+    <requirement type="package" version="0.2.1">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
   <![CDATA[
@@ -31,5 +31,6 @@
   </outputs>
   <citations>
     <citation type="doi">10.1101/172858</citation>
+    <citation type="doi">10.1099/mgen.0.000146</citation>
   </citations>
 </tool>
diff -r 8d01e55c32eb -r 965d2420eebf data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml
--- a/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml	Wed Mar 07 14:52:44 2018 -0500
+++ b/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml	Wed Mar 14 19:23:41 2018 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
-<tool id="mentalist_download_cgmlst" name="MentaLiST Download from cgMLST" tool_type="manage_data" version="0.1.4">
+<tool id="mentalist_download_cgmlst" name="MentaLiST Download from cgMLST" tool_type="manage_data" version="0.2.1">
   <requirements>
-    <requirement type="package" version="0.1.4">mentalist</requirement>
+    <requirement type="package" version="0.2.1">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
     <![CDATA[
@@ -20,6 +20,8 @@
       <option value="Clostridioides difficile">Clostridioides difficile</option>
       <option value="Enterococcus faecium">Enterococcus faecium</option>
       <option value="Francisella tularensis">Francisella tularensis</option>
+      <option value="Klebsiella pneumoniae/variicola/quasipneumoniae">Klebsiella pneumoniae/variicola/quasipneumoniae</option>
+      <option value="Mycobacterium tuberculosis/bovis/africanum/canettii">Mycobacterium tuberculosis/bovis/africanum/canettii</option>
       <option value="Legionella pneumophila">Legionella pneumophila</option>
       <option value="Listeria monocytogenes">Listeria monocytogenes</option>
       <option value="Staphylococcus aureus">Staphylococcus aureus</option>
@@ -30,5 +32,6 @@
   </outputs>
   <citations>
     <citation type="doi">10.1101/172858</citation>
+    <citation type="doi">10.1099/mgen.0.000146</citation>
   </citations>
 </tool>
diff -r 8d01e55c32eb -r 965d2420eebf data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml
--- a/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml	Wed Mar 07 14:52:44 2018 -0500
+++ b/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml	Wed Mar 14 19:23:41 2018 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
-<tool id="mentalist_download_enterobase" name="MentaLiST Download from Enterobase" tool_type="manage_data" version="0.1.4">
+<tool id="mentalist_download_enterobase" name="MentaLiST Download from Enterobase" tool_type="manage_data" version="0.2.1">
   <requirements>
-    <requirement type="package" version="0.1.4">mentalist</requirement>
+    <requirement type="package" version="0.2.1">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
     <![CDATA[
diff -r 8d01e55c32eb -r 965d2420eebf data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml
--- a/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml	Wed Mar 07 14:52:44 2018 -0500
+++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml	Wed Mar 14 19:23:41 2018 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
-<tool id="mentalist_download_pubmlst" name="MentaLiST Download from pubMLST" tool_type="manage_data" version="0.1.4">
+<tool id="mentalist_download_pubmlst" name="MentaLiST Download from pubMLST" tool_type="manage_data" version="0.2.1">
   <requirements>
-    <requirement type="package" version="0.1.4">mentalist</requirement>
+    <requirement type="package" version="0.2.1">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
     <![CDATA[
@@ -76,6 +76,7 @@
       <option value="Helicobacter pylori">Helicobacter pylori</option>
       <option value="Helicobacter suis">Helicobacter suis</option>
       <option value="Kingella kingae">Kingella kingae</option>
+      <option value="Klebsiella aerogenes">Klebsiella aerogenes</option>
       <option value="Klebsiella oxytoca">Klebsiella oxytoca</option>
       <option value="Klebsiella pneumoniae">Klebsiella pneumoniae</option>
       <option value="Kudoa septempunctata">Kudoa septempunctata</option>
@@ -155,5 +156,6 @@
   </outputs>
   <citations>
     <citation type="doi">10.1101/172858</citation>
+    <citation type="doi">10.1099/mgen.0.000146</citation>
   </citations>
 </tool>
diff -r 8d01e55c32eb -r 965d2420eebf tools/mentalist_call/mentalist_call.xml
--- a/tools/mentalist_call/mentalist_call.xml	Wed Mar 07 14:52:44 2018 -0500
+++ b/tools/mentalist_call/mentalist_call.xml	Wed Mar 14 19:23:41 2018 -0400
@@ -1,7 +1,10 @@
-<tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.1.4">
+<tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.2.1">
   <requirements>
-    <requirement type="package" version="0.1.4">mentalist</requirement>
+    <requirement type="package" version="0.2.1">mentalist</requirement>
   </requirements>
+  <edam_operations>
+    <edam_operation>operation_3840</edam_operation>
+  </edam_operations>
   <command detect_errors="exit_code"><![CDATA[
     mentalist
     call
@@ -35,10 +38,12 @@
   </inputs>
   <outputs>
     <data name="output_file" format="tabular"/>
+    <data name="coverage_file" format="tabular"/>
   </outputs>
   <help><![CDATA[
   ]]></help>
   <citations>
     <citation type="doi">10.1101/172858</citation>
+    <citation type="doi">10.1099/mgen.0.000146</citation>
   </citations>
 </tool>