From 72c3b8cb89129c6049bd4f534ba4bac6ef67bf35 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 13 Jul 2010 10:44:45 -0400
Subject: [PATCH] Enhance VCF to MAF error message when no input file is
 provided.

---
 tools/maf/vcf_to_maf_customtrack.py  |  4 ++++
 tools/maf/vcf_to_maf_customtrack.xml | 10 ++++++++--
 2 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/tools/maf/vcf_to_maf_customtrack.py b/tools/maf/vcf_to_maf_customtrack.py
index da193dd46c6..8a65a67c808 100644
--- a/tools/maf/vcf_to_maf_customtrack.py
+++ b/tools/maf/vcf_to_maf_customtrack.py
@@ -1,5 +1,6 @@
 #Dan Blankenberg
 from optparse import OptionParser
+import sys
 import galaxy_utils.sequence.vcf
 
 from galaxy import eggs
@@ -57,11 +58,14 @@ def main():
     parser.add_option( "-p", "--population", action="store_true", dest="population", default=False, help="Create MAF on a per population basis")
     parser.add_option( "-s", "--sample", action="store_true", dest="sample", default=False, help="Create MAF on a per sample basis")
     parser.add_option( "-n", "--name", dest="name", default='Unknown Custom Track', help="Name for Custom Track")
+    parser.add_option( "-g", "--galaxy", action="store_true", dest="galaxy", default=False, help="Tool is being executed by Galaxy (adds extra error messaging).")
     
 
     ( options, args ) = parser.parse_args()
     
     if len ( args ) < 3:
+        if options.galaxy:
+            print >>sys.stderr, "It appears that you forgot to specify an input VCF file, click 'Add new VCF...' to add at least input.\n"
         parser.error( "Need to specify an output file, a dbkey and at least one input file" )
     
     if not ( options.population ^ options.sample ):
diff --git a/tools/maf/vcf_to_maf_customtrack.xml b/tools/maf/vcf_to_maf_customtrack.xml
index 6ad5309c9ab..1d572f0ada2 100644
--- a/tools/maf/vcf_to_maf_customtrack.xml
+++ b/tools/maf/vcf_to_maf_customtrack.xml
@@ -1,13 +1,19 @@
 <tool id="vcf_to_maf_customtrack1" name="VCF to MAF Custom Track">
   <description>for display at UCSC</description>
-  <command interpreter="python">vcf_to_maf_customtrack.py $out_file1 ${vcf_source_type.vcf_file[0].vcf_input.dbkey} ${vcf_source_type.vcf_source} -n '$track_name'
-    ##
+  <command interpreter="python">vcf_to_maf_customtrack.py '$out_file1'
+    #if $vcf_source_type.vcf_file
+    '${vcf_source_type.vcf_file[0].vcf_input.dbkey}'
+    #else
+    '?'
+    #end if
+    ${vcf_source_type.vcf_source} -n '$track_name'
     #for $vcf_repeat in $vcf_source_type.vcf_file
     '${vcf_repeat.vcf_input}'
     #if $vcf_source_type.vcf_source == '-p'
       '${vcf_repeat.population_name}'
     #end if
     #end for
+    -g
   </command>
   <inputs>
     <param name="track_name" type="text" label="Custom Track Name" value="Galaxy Custom Track" size="30" />