From 6a892b3555a642c87cc5ee6b2304da33433284e0 Mon Sep 17 00:00:00 2001
From: Ross Lazarus <ross.lazarus@gmail.com>
Date: Fri, 26 Oct 2012 16:00:13 +1100
Subject: [PATCH] Fix parameters for fastqc to work properly with bam and with
 a contaminants file Been b0rken for a long time - probably not much used..

---
 lib/galaxy/tools/parameters/basic.py | 2 +-
 tools/filters/sorter.xml             | 2 +-
 tools/rgenetics/rgFastQC.py          | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index b1d515967ab..a6126e12a82 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -911,7 +911,7 @@ class ColumnListParameter( SelectToolParameter ):
         self.ref_input = None
         self.default_value = elem.get( "default_value", None )
         self.is_dynamic = True
-        self.usecolnames = string_as_bool( elem.get( "use_header_names", False ))
+        self.usecolnames = string_as_bool( elem.get( "use_header_names", True )) # much easier for the user - make default if not overridden
 
     def from_html( self, value, trans=None, context={} ):
         """
diff --git a/tools/filters/sorter.xml b/tools/filters/sorter.xml
index e176f6d8428..bd35d265017 100644
--- a/tools/filters/sorter.xml
+++ b/tools/filters/sorter.xml
@@ -15,7 +15,7 @@
   </command>
   <inputs>
     <param format="tabular" name="input" type="data" label="Sort Query" />
-    <param name="column" label="on column" type="data_column" data_ref="input" accept_default="true" />
+    <param name="column" label="on column" type="data_column" data_ref="input" accept_default="true"/>
     <param name="style" type="select" label="with flavor">
       <option value="num">Numerical sort</option>
       <option value="alpha">Alphabetical sort</option>
diff --git a/tools/rgenetics/rgFastQC.py b/tools/rgenetics/rgFastQC.py
index 31336ea19d9..3fa071b3a12 100644
--- a/tools/rgenetics/rgFastQC.py
+++ b/tools/rgenetics/rgFastQC.py
@@ -51,9 +51,9 @@ class FastQC():
         fastq = os.path.basename(self.opts.input)
         cl = [self.opts.executable,'--outdir=%s' % self.opts.outputdir]
         if self.opts.informat in ['sam','bam']:
-            cl.append('-f %s' % self.opts.informat)
+            cl.append('--f=%s' % self.opts.informat)
         if self.opts.contaminants <> None :
-            cl.append('-c %s' % self.opts.contaminants)
+            cl.append('--contaminants=%s' % self.opts.contaminants)
         # patch suggested by bwlang https://bitbucket.org/galaxy/galaxy-central/pull-request/30
 	# use a symlink in a temporary directory so that the FastQC report reflects the history input file name
         fastqinfilename = re.sub(ur'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(self.opts.inputfilename))