# HG changeset patch
# User dfornika
# Date 1508363472 14400
# Node ID 01d50d174dbbdae471e3eef50b537485e59b0713
# Parent  b9dfa8aa503da45569fb55a3938b59a7e8911b83
planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 71cef9adab4b246fee6d7f99e30562e850ffebfd

diff -r b9dfa8aa503d -r 01d50d174dbb data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.py
--- a/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.py	Thu Oct 12 19:13:11 2017 -0400
+++ b/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.py	Wed Oct 18 17:51:12 2017 -0400
@@ -3,6 +3,7 @@
 from __future__ import print_function
 
 import argparse
+import datetime
 import errno
 import os
 import string
@@ -18,10 +19,11 @@
 def mentalist_download_cgmlst( data_manager_dict, kmer_size, scheme, params, target_directory, data_table_names=DEFAULT_DATA_TABLE_NAMES ):
     translation_table = string.maketrans(string.punctuation, ("_" * 32))
     base_path = scheme.lower().replace(" ", "_").translate(translation_table) + "_cgmlst"
-    scheme_files_path = base_path + "_scheme"
-    database_path = base_path + "_k" + str(kmer_size)
-    database_name = base_path + "_k" + str(kmer_size) + ".jld"
-    display_name = scheme + " k=" + str(kmer_size) + " (PubMLST)"
+    today = datetime.date.today().isoformat()
+    scheme_files_path = base_path + "_scheme_" + today
+    database_path = base_path + "_k" + str(kmer_size) + "_" + today
+    database_name = base_path + "_k" + str(kmer_size) + "_" + today + ".jld"
+    display_name = scheme + " k=" + str(kmer_size) + " (cgMLST) " + today
     args = [ 'mentalist', 'download_cgmlst', '-s', scheme, '-k', str(kmer_size), '--db', database_name, '-o', scheme_files_path]
     proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
     return_code = proc.wait()
diff -r b9dfa8aa503d -r 01d50d174dbb data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py
--- a/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py	Thu Oct 12 19:13:11 2017 -0400
+++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py	Wed Oct 18 17:51:12 2017 -0400
@@ -18,10 +18,11 @@
 def mentalist_download_pubmlst( data_manager_dict, kmer_size, scheme, params, target_directory, data_table_names=DEFAULT_DATA_TABLE_NAMES ):
     translation_table = string.maketrans(string.punctuation, ("_" * 32))
     base_path = scheme.lower().replace(" ", "_").translate(translation_table) + "_pubmlst"
-    scheme_files_path = base_path + "_scheme"
-    database_path = base_path + "_k" + str(kmer_size)
-    database_name = base_path + "_k" + str(kmer_size) + ".jld"
-    display_name = scheme + " k=" + str(kmer_size) + " (PubMLST)"
+    today = datetime.date.today().isoformat()
+    scheme_files_path = base_path + "_scheme_" + today
+    database_path = base_path + "_k" + str(kmer_size) + "_" + today
+    database_name = base_path + "_k" + str(kmer_size) + "_" + today + ".jld"
+    display_name = scheme + " k=" + str(kmer_size) + " (PubMLST)" + today
     args = [ 'mentalist', 'download_pubmlst', '-s', scheme, '-k', str(kmer_size), '--db', database_name, '-o', scheme_files_path]
     proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
     return_code = proc.wait()
diff -r b9dfa8aa503d -r 01d50d174dbb tools/mentalist_call/mentalist_call.xml
--- a/tools/mentalist_call/mentalist_call.xml	Thu Oct 12 19:13:11 2017 -0400
+++ b/tools/mentalist_call/mentalist_call.xml	Wed Oct 18 17:51:12 2017 -0400
@@ -6,16 +6,24 @@
     mentalist
     call
     -o '$output_file'
-    -s '$sample_name'
     --db '$kmer_db.fields.path'
     #if $discard_threshold
         -t '$discard_threshold'
     #end if
-    $input_fastqs.forward $input_fastqs.reverse
+    #if '$fastq_input_selector' == "single"
+        -s '$fastq_input1.name'
+        '$fastq_input1'
+    #end if
+    #if '$fastq_input_selector' == "paired"
+        -s '$fastq_input1.name'
+        '$fastq_input1' '$fastq_input2'
+    #end if
+    #if '$fastq_input_selector' == "paired_collection"
+        -s '$fastq_input.name'
+        '$fastq_input.forward' '$fastq_input.reverse'
+    #end if
   ]]></command>
   <inputs>
-    <param name="sample_name" type="text"
-	   label="Sample Name" help="Sample Name" />
     <param name="kmer_db" type="select">
       <options from_data_table="mentalist_databases">
 	<validator type="no_options" message="No MentaLiST databases are available" />
@@ -27,11 +35,26 @@
     <param name="skip_length" type="integer"
 	   label="Skip Length" help="Skip length between consecutive k-mers."
 	   value="1" min="1" max="32" />
-    <param name="input_fastqs" type="data_collection" collection_type="paired" format="fastq"
-	   label="Input FastQ" help="FastQ input files" />
+    <conditional name="fastq_input">
+      <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
+	<option value="paired">Paired</option>
+	<option value="single">Single</option>
+	<option value="paired_collection">Paired Collection</option>
+      </param>
+      <when value="paired">
+	<param name="fastq_input1" type="data" format="fastq" label="Select first set of reads" help="Specify dataset with forward reads"/>
+	<param name="fastq_input2" type="data" format="fastq" label="Select second set of reads" help="Specify dataset with reverse reads"/>
+      </when>
+      <when value="single">
+	<param name="fastq_input1" type="data" format="fastq" label="Select fastq dataset" help="Specify dataset with single reads"/>
+      </when>
+      <when value="paired_collection">
+	<param name="fastq_input" format="fastq" type="data_collection" collection_type="paired" label="Select a paired collection" label="Select dataset pair" help="Specify paired dataset collection containing paired reads"/>
+      </when>
+    </conditional>
   </inputs>
   <outputs>
-    <data name="output_file" format="tsv"/>
+    <data name="output_file" format="tabular"/>
   </outputs>
   <help><![CDATA[
   ]]></help>