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changeset 46:210d15ce654a draft

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planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit c09044db42aa487678d7c8dd749fdf4a91ac1c75-dirty
author dfornika
date Wed, 02 May 2018 14:48:29 -0400
parents ec9bc05b331b
children f195dcb844a9
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.xml data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml tools/mentalist_call/mentalist_call.xml
diffstat 6 files changed, 19 insertions(+), 21 deletions(-) [+]
line wrap: on
line diff
--- a/data_managers/data_manager_conf.xml	Wed Apr 11 13:38:46 2018 -0400
+++ b/data_managers/data_manager_conf.xml	Wed May 02 14:48:29 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="0.1.5">
+  <data_manager tool_file="data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml" id="mentalist_build_db" version="0.1.7">
     <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="0.1.5">
+  <data_manager tool_file="data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml" id="mentalist_download_cgmlst" version="0.1.7">
     <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="0.1.5">
+  <data_manager tool_file="data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml" id="mentalist_download_pubmlst" version="0.1.7">
     <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="0.1.5">
+  <data_manager tool_file="data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml" id="mentalist_download_enterobase" version="0.1.7">
     <data_table name="mentalist_databases">
       <output>
         <column name="value" />
--- a/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml	Wed Apr 11 13:38:46 2018 -0400
+++ b/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml	Wed May 02 14:48:29 2018 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
-<tool id="mentalist_build_db" name="MentaLiST Build DB" tool_type="manage_data" version="0.1.5">
+<tool id="mentalist_build_db" name="MentaLiST Build DB" tool_type="manage_data" version="0.1.7">
   <requirements>
-    <requirement type="package" version="0.1.5">mentalist</requirement>
+    <requirement type="package" version="0.1.7">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
   <![CDATA[
@@ -30,6 +30,6 @@
     <data name="out_file" format="data_manager_json" />
   </outputs>
   <citations>
-    <citation type="doi">10.1099/mgen.0.000146</citation>
+    <citation type="doi">10.1101/172858</citation>
   </citations>
 </tool>
--- a/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml	Wed Apr 11 13:38:46 2018 -0400
+++ b/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml	Wed May 02 14:48:29 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="0.1.5">
+<tool id="mentalist_download_cgmlst" name="MentaLiST Download from cgMLST" tool_type="manage_data" version="0.1.7">
   <requirements>
-    <requirement type="package" version="0.1.5">mentalist</requirement>
+    <requirement type="package" version="0.1.7">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
     <![CDATA[
@@ -20,10 +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="Legionella pneumophila">Legionella pneumophila</option>
       <option value="Listeria monocytogenes">Listeria monocytogenes</option>
-      <option value="Mycobacterium tuberculosis/bovis/africanum/canettii">Mycobacterium tuberculosis/bovis/africanum/canettii</option>
       <option value="Staphylococcus aureus">Staphylococcus aureus</option>
     </param>
   </inputs>
@@ -31,6 +29,6 @@
     <data name="out_file" format="data_manager_json" />
   </outputs>
   <citations>
-    <citation type="doi">10.1099/mgen.0.000146</citation>
+    <citation type="doi">10.1101/172858</citation>
   </citations>
 </tool>
--- a/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml	Wed Apr 11 13:38:46 2018 -0400
+++ b/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml	Wed May 02 14:48:29 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="0.1.5">
+<tool id="mentalist_download_enterobase" name="MentaLiST Download from Enterobase" tool_type="manage_data" version="0.1.7">
   <requirements>
-    <requirement type="package" version="0.1.5">mentalist</requirement>
+    <requirement type="package" version="0.1.7">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
     <![CDATA[
@@ -30,6 +30,6 @@
     <data name="out_file" format="data_manager_json" />
   </outputs>
   <citations>
-    <citation type="doi">10.1099/mgen.0.000146</citation>
+    <citation type="doi">10.1101/172858</citation>
   </citations>
 </tool>
--- a/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml	Wed Apr 11 13:38:46 2018 -0400
+++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml	Wed May 02 14:48:29 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="0.1.5">
+<tool id="mentalist_download_pubmlst" name="MentaLiST Download from pubMLST" tool_type="manage_data" version="0.1.7">
   <requirements>
-    <requirement type="package" version="0.1.5">mentalist</requirement>
+    <requirement type="package" version="0.1.7">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
     <![CDATA[
@@ -154,6 +154,6 @@
     <data name="out_file" format="data_manager_json" />
   </outputs>
   <citations>
-    <citation type="doi">10.1099/mgen.0.000146</citation>
+    <citation type="doi">10.1101/172858</citation>
   </citations>
 </tool>
--- a/tools/mentalist_call/mentalist_call.xml	Wed Apr 11 13:38:46 2018 -0400
+++ b/tools/mentalist_call/mentalist_call.xml	Wed May 02 14:48:29 2018 -0400
@@ -1,6 +1,6 @@
-<tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.1.5">
+<tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.1.7">
   <requirements>
-    <requirement type="package" version="0.1.5">mentalist</requirement>
+    <requirement type="package" version="0.1.7">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
     mentalist
@@ -39,6 +39,6 @@
   <help><![CDATA[
   ]]></help>
   <citations>
-    <citation type="doi">10.1099/mgen.0.000146</citation>
+    <citation type="doi">10.1101/172858</citation>
   </citations>
 </tool>