Use from_work_dir instead of copying output files line by line. Write velvetg output to stdout.

tools/sr_assembly/velvetg.xml

@@ -4,7 +4,6 @@
   <command interpreter="python">
     velvetg_wrapper.py 
            '$input.extra_files_path'
-           '$contigs' '$stats' '$LastGraph' '$velvet_asm' '$unused_reads_fasta'
            #if $generate_amos.afg  == "yes":
                -amos_file $generate_amos.afg
            #end if
@@ -169,20 +168,17 @@
     </conditional>
   </inputs>
   <outputs>
-    <!--
-    <data format="velvet_graph" name="LastGraph" />
-    -->
-    <data format="txt" name="LastGraph" label="${tool.name} on ${on_string}: LastGraph">
+    <data format="txt" name="LastGraph" label="${tool.name} on ${on_string}: LastGraph" from_work_dir="LastGraph">
       <filter>last_graph['generate_graph'] == "yes"</filter>
     </data>
-    <data format="afg" name="velvet_asm" label="${tool.name} on ${on_string}: AMOS.afg">
+    <data format="afg" name="velvet_asm" label="${tool.name} on ${on_string}: AMOS.afg" from_work_dir="velvet_asm.afg">
       <filter>generate_amos['afg'] == "yes"</filter>
     </data>
-    <data format="fasta" name="unused_reads_fasta" label="${tool.name} on ${on_string}: Unused Reads">
+    <data format="fasta" name="unused_reads_fasta" label="${tool.name} on ${on_string}: Unused Reads" from_work_dir="UnusedReads.fa">
       <filter>unused_reads['generate_unused'] == "yes"</filter>
     </data>
-    <data format="tabular" name="stats" label="${tool.name} on ${on_string}: Stats"/>
-    <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs"/>
+    <data format="tabular" name="stats" label="${tool.name} on ${on_string}: Stats" from_work_dir="stats.txt" />
+    <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="contigs.fa" />
   </outputs>
   <requirements>
     <requirement type="package">velvet</requirement>

tools/sr_assembly/velvetg_wrapper.py

@@ -4,14 +4,9 @@
 Classes encapsulating decypher tool.
 James E Johnson - University of Minnesota
 """
-import pkg_resources;
-import logging, os, string, sys, tempfile, glob, shutil, types, urllib
-import shlex, subprocess
-from optparse import OptionParser, OptionGroup
-from stat import *
-
-
-log = logging.getLogger( __name__ )
+import os
+import sys
+import subprocess
 
 assert sys.version_info[:2] >= ( 2, 4 )
 
@@ -19,20 +14,15 @@ def stop_err( msg ):
     sys.stderr.write( "%s\n" % msg )
     sys.exit()
 
+
 def __main__():
     #Parse Command Line
-    s = 'velvetg_wrapper.py:  argv = %s\n' % (sys.argv)
-    # print >> sys.stderr, s # so will appear as blurb for file
-    argcnt = len(sys.argv)
     working_dir = sys.argv[1]
-    contigs = sys.argv[2]
-    stats = sys.argv[3]
-    LastGraph = sys.argv[4]
-    afgFile = sys.argv[5]
-    unusedReadsFile = sys.argv[6]
-    inputs = string.join(sys.argv[7:],' ')
-    cmdline = 'velvetg %s %s > /dev/null' % (working_dir, inputs)
-    # print >> sys.stderr, cmdline # so will appear as blurb for file
+    inputs = ' '.join(sys.argv[2:])
+    for _ in ('Roadmaps', 'Sequences'):
+        os.symlink(os.path.join(working_dir, _), _)
+    cmdline = 'velvetg . %s' % (inputs)
+    print "Command to be executed: %s" % cmdline
     try:
         proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE )
         returncode = proc.wait()
@@ -50,41 +40,7 @@ def __main__():
             raise Exception, stderr
     except Exception, e:
         stop_err( 'Error running velvetg ' + str( e ) )
-    out = open(contigs,'w')
-    contigs_path = os.path.join(working_dir,'contigs.fa')
-    for line in open( contigs_path ):
-        out.write( "%s" % (line) )
-    out.close()
-    out = open(stats,'w')
-    stats_path = os.path.join(working_dir,'stats.txt')
-    for line in open( stats_path ):
-        out.write( "%s" % (line) )
-    out.close()
-    if LastGraph != 'None':
-        out = open(LastGraph,'w')
-        LastGraph_path = os.path.join(working_dir,'LastGraph')
-        for line in open( LastGraph_path ):
-            out.write( "%s" % (line) )
-        out.close()
-    if afgFile != 'None':
-        out = open(afgFile,'w')
-        afgFile_path = os.path.join(working_dir,'velvet_asm.afg')
-        try:
-            for line in open( afgFile_path ):
-                out.write( "%s" % (line) )
-        except:
-            logging.warn( 'error reading %s' %(afgFile_path))
-            pass
-        out.close()
-    if unusedReadsFile != 'None':
-        out = open(unusedReadsFile,'w')
-        unusedReadsFile_path = os.path.join(working_dir,'UnusedReads.fa')
-        try:
-            for line in open( unusedReadsFile_path ):
-                out.write( "%s" % (line) )
-        except:
-            logging.info( 'error reading %s' %(unusedReadsFile_path))
-            pass
-        out.close()
 
-if __name__ == "__main__": __main__()
+
+if __name__ == "__main__":
+    __main__()