diff run_skesa_collection.py @ 19:abb622c228c4 draft

planemo upload commit 1e3adef29c2d50fa89df02d0153e069c4328557e

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/run_skesa_collection.py	Mon Aug 27 08:59:02 2018 -0400
@@ -0,0 +1,43 @@
+import sys
+
+from pathlib import Path
+
+path1 = sys.argv[1]
+
+cores = sys.argv[2]
+
+memory = sys.argv[2]
+
+print(path1)
+
+#print(path2)
+
+pathlist = Path(path1).glob('*fastq*')
+
+i = 0
+skcmd = []
+
+skcmd.append("skesa ")
+
+for path in pathlist:
+    # because path is object not string-wq
+    i += 1
+    path_in_str = str(path)
+    if i == 2:
+        skcmd.append("," + path_in_str)
+        #print("," + path_in_str)
+        i = 0
+    if i == 1:
+        skcmd.append(" --fastq " + path_in_str)
+        #print(" --fastq " + path_in_str) 
+
+    
+
+if cores != 0:
+    skcmd.append(" --cores " + cores)
+    
+
+skcmd.append(" --memory " + memory)
+
+skcmds = ''.join(skcmd)
+print(skcmds)