# HG changeset patch
# User dfornika
# Date 1523396325 14400
# Node ID f7c4ccfa3ba90d91c6641984aa69fae6507b1b7c
# Parent  b3856a35b527a33cbed885115d891c0030ce9e50
planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit f161d96d4d4dcd11a53eeda99595d5fd22891612-dirty

diff -r b3856a35b527 -r f7c4ccfa3ba9 data_managers/data_manager_conf.xml
--- a/data_managers/data_manager_conf.xml	Thu Mar 29 14:55:23 2018 -0400
+++ b/data_managers/data_manager_conf.xml	Tue Apr 10 17:38:45 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="0.2.2">
+  <data_manager tool_file="data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml" id="mentalist_build_db" version="0.1.5">
     <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="0.2.2">
+  <data_manager tool_file="data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml" id="mentalist_download_cgmlst" version="0.1.5">
     <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="0.2.2">
+  <data_manager tool_file="data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml" id="mentalist_download_pubmlst" version="0.1.5">
     <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="0.2.2">
+  <data_manager tool_file="data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml" id="mentalist_download_enterobase" version="0.1.5">
     <data_table name="mentalist_databases">
       <output>
         <column name="value" />
diff -r b3856a35b527 -r f7c4ccfa3ba9 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	Thu Mar 29 14:55:23 2018 -0400
+++ b/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml	Tue Apr 10 17:38:45 2018 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
-<tool id="mentalist_build_db" name="MentaLiST Build DB" tool_type="manage_data" version="0.2.2">
+<tool id="mentalist_build_db" name="MentaLiST Build DB" tool_type="manage_data" version="0.1.5">
   <requirements>
-    <requirement type="package" version="0.2.2">mentalist</requirement>
+    <requirement type="package" version="0.1.5">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
   <![CDATA[
@@ -30,7 +30,6 @@
     <data name="out_file" format="data_manager_json" />
   </outputs>
   <citations>
-    <citation type="doi">10.1101/172858</citation>
     <citation type="doi">10.1099/mgen.0.000146</citation>
   </citations>
 </tool>
diff -r b3856a35b527 -r f7c4ccfa3ba9 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	Thu Mar 29 14:55:23 2018 -0400
+++ b/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml	Tue Apr 10 17:38:45 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="0.2.2">
+<tool id="mentalist_download_cgmlst" name="MentaLiST Download from cgMLST" tool_type="manage_data" version="0.1.5">
   <requirements>
-    <requirement type="package" version="0.2.2">mentalist</requirement>
+    <requirement type="package" version="0.1.5">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
     <![CDATA[
@@ -16,22 +16,21 @@
 	   label="Kmer size" help="Kmer size"
 	   value="31" min="1" max="32" />
     <param name="scheme" type="select" multiple="false" label="Select scheme to download">
-      <option value="Acinetobacter baumannii">Acinetobacter baumannii</option>
-      <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>
+      <option value="3956907">Acinetobacter baumannii</option>
+      <option value="3560802">Clostridioides difficile</option>
+      <option value="991893">Enterococcus faecium</option>
+      <option value="260204">Francisella tularensis</option>
+      <option value="2187931">Klebsiella pneumoniae/variicola/quasipneumoniae</option>
+      <option value="1025099">Legionella pneumophila</option>
+      <option value="690488">Listeria monocytogenes</option>
+      <option value="741110">Mycobacterium tuberculosis/bovis/africanum/canettii</option>
+      <option value="141106">Staphylococcus aureus</option>
     </param>
   </inputs>
   <outputs>
     <data name="out_file" format="data_manager_json" />
   </outputs>
   <citations>
-    <citation type="doi">10.1101/172858</citation>
     <citation type="doi">10.1099/mgen.0.000146</citation>
   </citations>
 </tool>
diff -r b3856a35b527 -r f7c4ccfa3ba9 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	Thu Mar 29 14:55:23 2018 -0400
+++ b/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml	Tue Apr 10 17:38:45 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="0.2.2">
+<tool id="mentalist_download_enterobase" name="MentaLiST Download from Enterobase" tool_type="manage_data" version="0.1.5">
   <requirements>
-    <requirement type="package" version="0.2.2">mentalist</requirement>
+    <requirement type="package" version="0.1.5">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
     <![CDATA[
diff -r b3856a35b527 -r f7c4ccfa3ba9 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	Thu Mar 29 14:55:23 2018 -0400
+++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml	Tue Apr 10 17:38:45 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="0.2.2">
+<tool id="mentalist_download_pubmlst" name="MentaLiST Download from pubMLST" tool_type="manage_data" version="0.1.5">
   <requirements>
-    <requirement type="package" version="0.2.2">mentalist</requirement>
+    <requirement type="package" version="0.1.5">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>
@@ -156,6 +155,5 @@
   </outputs>
   <citations>
     <citation type="doi">10.1101/172858</citation>
-    <citation type="doi">10.1099/mgen.0.000146</citation>
   </citations>
 </tool>
diff -r b3856a35b527 -r f7c4ccfa3ba9 tools/mentalist_call/mentalist_call.xml
--- a/tools/mentalist_call/mentalist_call.xml	Thu Mar 29 14:55:23 2018 -0400
+++ b/tools/mentalist_call/mentalist_call.xml	Tue Apr 10 17:38:45 2018 -0400
@@ -1,23 +1,16 @@
-<tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.2.2">
+<tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.1.5">
   <requirements>
-    <requirement type="package" version="0.2.2">mentalist</requirement>
+    <requirement type="package" version="0.1.5">mentalist</requirement>
   </requirements>
-  <edam_operations>
-    <edam_operation>operation_3840</edam_operation>
-  </edam_operations>
   <command detect_errors="exit_code"><![CDATA[
     mentalist
     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":
-      -1 $input_type.pInput1 -2 $input_type.pInput2
+       -s $input_type.pInput1.name $input_type.pInput1 $input_type.pInput2
     #elif $input_type.sPaired == "collections":
-      -1 $input_type.fastq_collection.forward -2 $input_type.fastq_collection.reverse
+       -s $input_type.fastq_collection.name $input_type.fastq_collection.forward $input_type.fastq_collection.reverse
     #end if
   ]]></command>
   <inputs>
@@ -39,27 +32,13 @@
 	<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" />
-    <param 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="coverage_file" format="tabular" />
+    <data name="output_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>