From 0b85ba75bb37b0b139972311694edce89fff11ca Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 24 May 2010 15:05:55 -0400
Subject: [PATCH] Minor cleanup for ensembl display applications and fastq
 masker tool.

---
 display_applications/ensembl/ensembl_gff.xml             | 6 ++----
 display_applications/ensembl/ensembl_interval_as_bed.xml | 6 ++----
 tool_conf.xml.main                                       | 1 +
 tools/fastq/fastq_masker_by_quality.py                   | 2 +-
 4 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/display_applications/ensembl/ensembl_gff.xml b/display_applications/ensembl/ensembl_gff.xml
index 449e016c7a6..26aec51b9b4 100644
--- a/display_applications/ensembl/ensembl_gff.xml
+++ b/display_applications/ensembl/ensembl_gff.xml
@@ -18,8 +18,7 @@
         
         <param type="data" name="gff_file" url="galaxy_${DATASET_HASH}.gff" />
         <param type="template" name="site_organism" strip="True" >
-            #set index = $site_dbkeys.index( $gff_file.dbkey )
-            $site_organisms[ $index ]
+            $site_organisms[ $site_dbkeys.index( $gff_file.dbkey ) ]
         </param>
         <param type="template" name="position" strip="True" >
 #set line_count = 0
@@ -82,8 +81,7 @@ ${chrom}:${start}-${end}
         
         <param type="data" name="gff_file" url="galaxy_${DATASET_HASH}.gff" />
         <param type="template" name="site_organism" strip="True" >
-            #set index = $site_dbkeys.index( $gff_file.dbkey )
-            $site_organisms[ $index ]
+            $site_organisms[ $site_dbkeys.index( $gff_file.dbkey ) ]
         </param>
         <param type="template" name="position" strip="True" >
             #set line_count = 0
diff --git a/display_applications/ensembl/ensembl_interval_as_bed.xml b/display_applications/ensembl/ensembl_interval_as_bed.xml
index ffa97fe0606..517f3b8aa55 100644
--- a/display_applications/ensembl/ensembl_interval_as_bed.xml
+++ b/display_applications/ensembl/ensembl_interval_as_bed.xml
@@ -18,8 +18,7 @@
         
         <param type="data" name="bed_file" url="galaxy_${DATASET_HASH}.bed" format="bedstrict"/>
         <param type="template" name="site_organism" strip="True" >
-            #set index = $site_dbkeys.index( $bed_file.dbkey )
-            $site_organisms[ $index ]
+            $site_organisms[ $site_dbkeys.index( $bed_file.dbkey ) ]
         </param>
         <param type="template" name="position" strip="True" >
 #set line_count = 0
@@ -82,8 +81,7 @@ ${chrom}:${start + 1}-${end}
         
         <param type="data" name="bed_file" url="galaxy_${DATASET_HASH}.bed" format="bedstrict"/>
         <param type="template" name="site_organism" strip="True" >
-            #set index = $site_dbkeys.index( $bed_file.dbkey )
-            $site_organisms[ $index ]
+            $site_organisms[ $site_dbkeys.index( $bed_file.dbkey ) ]
         </param>
         <param type="template" name="position" strip="True" >
             #set line_count = 0
diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index aa4323a25de..cdaa84a6cdc 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -298,6 +298,7 @@
         <tool file="fastq/fastq_filter.xml" />
         <tool file="fastq/fastq_trimmer.xml" />
         <tool file="fastq/fastq_trimmer_by_quality.xml" />
+        <tool file="fastq/fastq_masker_by_quality.xml" />
         <tool file="fastq/fastq_manipulation.xml" />
         <tool file="fastq/fastq_to_fasta.xml" />
         <tool file="fastq/fastq_to_tabular.xml" />
diff --git a/tools/fastq/fastq_masker_by_quality.py b/tools/fastq/fastq_masker_by_quality.py
index 12adb73765b..4e937dd2820 100644
--- a/tools/fastq/fastq_masker_by_quality.py
+++ b/tools/fastq/fastq_masker_by_quality.py
@@ -46,7 +46,7 @@ class BaseReplacer( object ):
 def main():
     usage = "usage: %prog [options] input_file output_file"
     parser = OptionParser( usage=usage )
-    parser.add_option( '-f', '--format', dest='format', type='choice', default='sanger', choices=( 'sanger', 'cssanger', 'solexa', 'illumina' ), help='FASTQ variant type' )
+    parser.add_option( '-f', '--format', dest='format', type='choice', default='sanger', choices=( 'sanger', 'solexa', 'illumina' ), help='FASTQ variant type' )
     parser.add_option( '-m', '--mask_character', dest='mask_character', default='N', help='Mask Character to use' )
     parser.add_option( '-c', '--score_comparison', type="choice", dest='score_comparison', default='le', choices=('gt','ge','eq','lt', 'le', 'ne' ), help='Mask base when score is' )
     parser.add_option( '-s', '--quality_score', type="float", dest='quality_score', default='0', help='Quality Score' )