# HG changeset patch
# User Bjoern Gruening <bjoern.gruening@gmail.com>
# Date 1370608853 -7200
# Node ID ce7228503d494d45741e075d6151366c3f01fd6f
# Parent  2d0c268856040cc2ca727ced0f03c196b55f2c45
changes

diff -r 2d0c26885604 -r ce7228503d49 glimmer3-build-icm-wrapper.xml
--- a/glimmer3-build-icm-wrapper.xml	Fri Jun 07 07:51:49 2013 -0400
+++ b/glimmer3-build-icm-wrapper.xml	Fri Jun 07 14:40:53 2013 +0200
@@ -18,7 +18,7 @@
                 --stop_codons "${stop_codon_opts.stop_codons}"
             #end if
 
-            $outfile &lt; $infile
+            $outfile &lt; $infile 2>&#38;1;
     </command>
     <inputs>
         <param name="infile" type="data" format="fasta" label="Trainings Dataset" help="A set of known genes in FASTA format." />
diff -r 2d0c26885604 -r ce7228503d49 glimmer_orf_to_seq.py
--- a/glimmer_orf_to_seq.py	Fri Jun 07 07:51:49 2013 -0400
+++ b/glimmer_orf_to_seq.py	Fri Jun 07 14:40:53 2013 +0200
@@ -5,7 +5,7 @@
 Author: Bjoern Gruening
 """
 import sys, os
-import Bio.SeqIO
+from Bio import SeqIO
 from Bio.SeqRecord import SeqRecord
 
 def glimmer2seq( glimmer_prediction = sys.argv [1], genome_sequence = sys.argv[2], outfile = sys.argv[3] ):
@@ -16,7 +16,7 @@
         print "Missing input values."
         sys.exit()
 
-    fastafile = Bio.SeqIO.parse(sequence, "fasta")
+    fastafile = SeqIO.parse(sequence, "fasta")
 
     sequences = dict()
     seq_records = list()
@@ -32,9 +32,9 @@
 
             orf_name = line[0:8]
             if orf_start <= orf_end:
-                seq_records.add( SeqRecord( entry.seq[ orf_start-1 : orf_end ], id = orf_name, description = entry.description ) )
+                seq_records.append( SeqRecord( entry.seq[ orf_start-1 : orf_end ], id = orf_name, description = entry.description ) )
             else:
-                seq_records.add( SeqRecord( entry.seq[ orf_end-1 : orf_start ].reverse_complement(), id = orf_name, description = entry.description ) )
+                seq_records.append( SeqRecord( entry.seq[ orf_end-1 : orf_start ].reverse_complement(), id = orf_name, description = entry.description ) )
 
     SeqIO.write( seq_records, outfile, "fasta" )
     glimmerfile.close()
diff -r 2d0c26885604 -r ce7228503d49 glimmer_predict.py
--- a/glimmer_predict.py	Fri Jun 07 07:51:49 2013 -0400
+++ b/glimmer_predict.py	Fri Jun 07 14:40:53 2013 +0200
@@ -62,7 +62,8 @@
         genome_seq_file, icm.name, os.path.join(tempdir, tag)], 
         stdout = subprocess.PIPE, stderr=subprocess.PIPE).communicate()
 
-    shutil.copyfile( os.path.join( tempdir, tag + ".predict" ), outfile_classic_glimmer )
+    if outfile_classic_glimmer.strip() != 'None':
+        shutil.copyfile( os.path.join( tempdir, tag + ".predict" ), outfile_classic_glimmer )
     if outfile_ext_path.strip() != 'None':
         shutil.copyfile( os.path.join( tempdir, tag + ".detail" ), outfile_ext_path )
 
diff -r 2d0c26885604 -r ce7228503d49 glimmer_predict.xml
--- a/glimmer_predict.xml	Fri Jun 07 07:51:49 2013 -0400
+++ b/glimmer_predict.xml	Fri Jun 07 14:40:53 2013 +0200
@@ -7,9 +7,13 @@
     <command interpreter="python">
         glimmer_predict.py 
             $input
-            $prediction
+            #if $report:
+                $prediction
+            #else:
+                "None"
+            #end if
             #if $detailed_report:
-                $output_ext
+                $detailed
             #else:
                 "None"
             #end if
diff -r 2d0c26885604 -r ce7228503d49 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Jun 07 07:51:49 2013 -0400
+++ b/tool_dependencies.xml	Fri Jun 07 14:40:53 2013 +0200
@@ -1,7 +1,7 @@
-<?xml version="1.0"?>
+<?xml version='1.0' encoding='utf-8'?>
 <tool_dependency>
     <package name="biopython" version="1.61">
-        <repository changeset_revision="e87f0c6897a8" name="package_biopython_1_61" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="e87f0c6897a8" name="package_biopython_1_61" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <set_environment version="1.0">
         <environment_variable action="set_to" name="GLIMMER_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
@@ -27,4 +27,4 @@
 Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA.
 http://www.cbcb.umd.edu/software/glimmer/</readme>
     </package>
-</tool_dependency>
+</tool_dependency>
\ No newline at end of file