Mercurial > repos > dfornika > mentalist

changeset 36:eb409f3f338d draft

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planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit e8fb3d5bf231b27e1ec9beabaefc99041d15fd25
author dfornika
date Sat, 24 Mar 2018 18:07:35 -0400
parents 32e67d162d19
children c7ae5215f11d
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, 14 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- a/data_managers/data_manager_conf.xml	Wed Mar 14 19:27:26 2018 -0400
+++ b/data_managers/data_manager_conf.xml	Sat Mar 24 18:07:35 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="0.2.1">
+  <data_manager tool_file="data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml" id="mentalist_build_db" version="master">
     <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="0.2.1">
+  <data_manager tool_file="data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml" id="mentalist_download_cgmlst" version="master">
     <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="0.2.1">
+  <data_manager tool_file="data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml" id="mentalist_download_pubmlst" version="master">
     <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="0.2.1">
+  <data_manager tool_file="data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml" id="mentalist_download_enterobase" version="master">
     <data_table name="mentalist_databases">
       <output>
         <column name="value" />
--- a/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml	Wed Mar 14 19:27:26 2018 -0400
+++ b/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml	Sat Mar 24 18:07:35 2018 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
-<tool id="mentalist_build_db" name="MentaLiST Build DB" tool_type="manage_data" version="0.2.1">
+<tool id="mentalist_build_db" name="MentaLiST Build DB" tool_type="manage_data" version="master">
   <requirements>
-    <requirement type="package" version="0.2.1">mentalist</requirement>
+    <requirement type="package" version="master">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
   <![CDATA[
--- a/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml	Wed Mar 14 19:27:26 2018 -0400
+++ b/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml	Sat Mar 24 18:07:35 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="0.2.1">
+<tool id="mentalist_download_cgmlst" name="MentaLiST Download from cgMLST" tool_type="manage_data" version="master">
   <requirements>
-    <requirement type="package" version="0.2.1">mentalist</requirement>
+    <requirement type="package" version="master">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
     <![CDATA[
@@ -20,8 +20,6 @@
       <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>
--- a/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml	Wed Mar 14 19:27:26 2018 -0400
+++ b/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml	Sat Mar 24 18:07:35 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="0.2.1">
+<tool id="mentalist_download_enterobase" name="MentaLiST Download from Enterobase" tool_type="manage_data" version="master">
   <requirements>
-    <requirement type="package" version="0.2.1">mentalist</requirement>
+    <requirement type="package" version="master">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
     <![CDATA[
--- a/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml	Wed Mar 14 19:27:26 2018 -0400
+++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml	Sat Mar 24 18:07:35 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="0.2.1">
+<tool id="mentalist_download_pubmlst" name="MentaLiST Download from pubMLST" tool_type="manage_data" version="master">
   <requirements>
-    <requirement type="package" version="0.2.1">mentalist</requirement>
+    <requirement type="package" version="master">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
     <![CDATA[
@@ -76,7 +76,6 @@
       <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>
--- a/tools/mentalist_call/mentalist_call.xml	Wed Mar 14 19:27:26 2018 -0400
+++ b/tools/mentalist_call/mentalist_call.xml	Sat Mar 24 18:07:35 2018 -0400
@@ -1,6 +1,6 @@
-<tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.2.1">
+<tool id="mentalist_call" name="MentaLiST MLST Analysis" version="master">
   <requirements>
-    <requirement type="package" version="0.2.1">mentalist</requirement>
+    <requirement type="package" version="master">mentalist</requirement>
   </requirements>
   <edam_operations>
     <edam_operation>operation_3840</edam_operation>
@@ -38,7 +38,6 @@
   </inputs>
   <outputs>
     <data name="output_file" format="tabular"/>
-    <data name="coverage_file" format="tabular"/>
   </outputs>
   <help><![CDATA[
   ]]></help>