diff glimmerHMM/glimmerhmm_to_sequence.py @ 0:c9699375fcf6 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/glimmerHMM/glimmerhmm_to_sequence.py	Wed Jul 13 10:55:48 2016 -0400
@@ -0,0 +1,29 @@
+#!/usr/bin/env python
+"""Convert GlimmerHMM gene predictions into protein sequences.
+
+This works with both the GFF and the costumn Tabular Output.
+And is only a wrapper to call the appropiate scripts.
+
+Usage:
+    glimmerhmm_to_sequence.py <glimmer output> <ref fasta> <output file> <format> <protein>
+
+"""
+import sys
+import os
+import glimmerhmm_tabular_to_sequence
+import glimmerhmm_gff_to_sequence
+
+def main(glimmer_file, ref_file, out_file, to_protein = False):
+    if to_protein == 'True':
+        to_protein = True
+    else:
+        to_protein = False
+
+    glimmerhmm_gff_to_sequence.main(glimmer_file, ref_file, out_file, to_protein)
+
+
+if __name__ == "__main__":
+    if len(sys.argv) != 5:
+        print __doc__
+        sys.exit()
+    main(*sys.argv[1:])