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

@@ -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={} ):
         """

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>

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))