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changeset 28:94eb129b6fb0 draft

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planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 4a5aaa4ca1558f498342682294a55d8b3a9c38d9
author dfornika
date Wed, 18 Oct 2017 18:31:14 -0400
parents 916ca1e73ec9
children 25baf4a4b98e
files data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py tools/mentalist_call/mentalist_call.xml
diffstat 2 files changed, 12 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- 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()
--- 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>