# HG changeset patch
# User dfornika
# Date 1521933800 14400
# Node ID c7ae5215f11d562178f76dc9788d6336bd98b098
# Parent  eb409f3f338d210828f8d8ae9842d9ad9967ddc1
planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 79b9f36868b2aaf72661abd09b96a3ad582b8918

diff -r eb409f3f338d -r c7ae5215f11d data_managers/data_manager_conf.xml
--- a/data_managers/data_manager_conf.xml	Sat Mar 24 18:07:35 2018 -0400
+++ b/data_managers/data_manager_conf.xml	Sat Mar 24 19:23:20 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="master">
+  <data_manager tool_file="data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml" id="mentalist_build_db" version="0.2.2">
     <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="master">
+  <data_manager tool_file="data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml" id="mentalist_download_cgmlst" version="0.2.2">
     <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="master">
+  <data_manager tool_file="data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml" id="mentalist_download_pubmlst" version="0.2.2">
     <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="master">
+  <data_manager tool_file="data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml" id="mentalist_download_enterobase" version="0.2.2">
     <data_table name="mentalist_databases">
       <output>
         <column name="value" />
diff -r eb409f3f338d -r c7ae5215f11d 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	Sat Mar 24 18:07:35 2018 -0400
+++ b/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml	Sat Mar 24 19:23:20 2018 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
-<tool id="mentalist_build_db" name="MentaLiST Build DB" tool_type="manage_data" version="master">
+<tool id="mentalist_build_db" name="MentaLiST Build DB" tool_type="manage_data" version="0.2.2">
   <requirements>
-    <requirement type="package" version="master">mentalist</requirement>
+    <requirement type="package" version="0.2.2">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
   <![CDATA[
diff -r eb409f3f338d -r c7ae5215f11d 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	Sat Mar 24 18:07:35 2018 -0400
+++ b/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml	Sat Mar 24 19:23:20 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="master">
+<tool id="mentalist_download_cgmlst" name="MentaLiST Download from cgMLST" tool_type="manage_data" version="0.2.2">
   <requirements>
-    <requirement type="package" version="master">mentalist</requirement>
+    <requirement type="package" version="0.2.2">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>
diff -r eb409f3f338d -r c7ae5215f11d 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	Sat Mar 24 18:07:35 2018 -0400
+++ b/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml	Sat Mar 24 19:23:20 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="master">
+<tool id="mentalist_download_enterobase" name="MentaLiST Download from Enterobase" tool_type="manage_data" version="0.2.2">
   <requirements>
-    <requirement type="package" version="master">mentalist</requirement>
+    <requirement type="package" version="0.2.2">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
     <![CDATA[
diff -r eb409f3f338d -r c7ae5215f11d 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	Sat Mar 24 18:07:35 2018 -0400
+++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml	Sat Mar 24 19:23:20 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="master">
+<tool id="mentalist_download_pubmlst" name="MentaLiST Download from pubMLST" tool_type="manage_data" version="0.2.2">
   <requirements>
-    <requirement type="package" version="master">mentalist</requirement>
+    <requirement type="package" version="0.2.2">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>
diff -r eb409f3f338d -r c7ae5215f11d tools/mentalist_call/mentalist_call.xml
--- a/tools/mentalist_call/mentalist_call.xml	Sat Mar 24 18:07:35 2018 -0400
+++ b/tools/mentalist_call/mentalist_call.xml	Sat Mar 24 19:23:20 2018 -0400
@@ -1,6 +1,6 @@
-<tool id="mentalist_call" name="MentaLiST MLST Analysis" version="master">
+<tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.2.2">
   <requirements>
-    <requirement type="package" version="master">mentalist</requirement>
+    <requirement type="package" version="0.2.2">mentalist</requirement>
   </requirements>
   <edam_operations>
     <edam_operation>operation_3840</edam_operation>
@@ -10,6 +10,10 @@
     call
     -o '$output_file'
     --db '$kmer_db.fields.path'
+    --mutation_threshold '$mutation_threshold'
+    --kt '$kmer_threshold'
+    $output_votes
+    $output_special
     #if $input_type.sPaired == "paired":
        -s $input_type.pInput1.name $input_type.pInput1 $input_type.pInput2
     #elif $input_type.sPaired == "collections":
@@ -35,9 +39,23 @@
 	<validator type="no_options" message="No MentaLiST databases are available" />
       </options>
     </param>
+    <param name="mutation_threshold" type="integer" label="Mutation threshold"
+	   help="Maximum number of mutations when looking for novel alleles."
+	   value="6" min="1" max="25" />
+    <param name="kmer_threshold" type="integer" label="Kmer threshold"
+	   help="Minimum number of times a kmer is seen to be considered present in the sample."
+	   value="10" min="1" max="25" />
+    <parapm name="output_votes" type="boolean" label="Output votes"
+	    argument="--output_votes" truevalue="--output_votes" falsevalue=""
+	    help="Outputs the results for the original voting algorithm" />
+    <param name="output_special" type="boolean" label="Output special"
+	   argument="--output_special" truevalue="--output_special" falsevalue=""
+	   help="Outputs a fasta file with the alleles from special cases such as incomplete coverage, novel and multiple alleles." />
+
   </inputs>
   <outputs>
-    <data name="output_file" format="tabular"/>
+    <data name="output_file" format="tabular" />
+    <data name="coverage_file" format="tabular" />
   </outputs>
   <help><![CDATA[
   ]]></help>