# HG changeset patch
# User dfornika
# Date 1508365874 14400
# Node ID 94eb129b6fb044c92c172ec86adf5276b4cfb636
# Parent  916ca1e73ec9e6b879a43bca3714ccd92966c872
planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 4a5aaa4ca1558f498342682294a55d8b3a9c38d9

diff -r 916ca1e73ec9 -r 94eb129b6fb0 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	Wed Oct 18 18:09:33 2017 -0400
+++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py	Wed Oct 18 18:31:14 2017 -0400
@@ -23,7 +23,7 @@
     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
+    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 916ca1e73ec9 -r 94eb129b6fb0 tools/mentalist_call/mentalist_call.xml
--- a/tools/mentalist_call/mentalist_call.xml	Wed Oct 18 18:09:33 2017 -0400
+++ b/tools/mentalist_call/mentalist_call.xml	Wed Oct 18 18:31:14 2017 -0400
@@ -10,17 +10,19 @@
     #if $discard_threshold
         -t '$discard_threshold'
     #end if
-    #if '$fastq_input_selector' == "single"
+    #if str( $fastq_input_selector ) == "single":
         -s '$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'
+    #else:
+        #if str( $fastq_input_selector ) == "paired":
+            -s '$fastq_input1.name'
+            '$fastq_input1' '$fastq_input2'
+	#else:
+            #if str( $fastq_input_selector ) == "paired_collection":
+                -s '$fastq_input.name'
+                '$fastq_input.forward' '$fastq_input.reverse'
+	    #end if
+	#end if	
     #end if
   ]]></command>
   <inputs>