diff --git a/datatypes_conf.xml.sample b/datatypes_conf.xml.sample
index d4bd296f331..79d610819e6 100644
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -123,7 +123,7 @@
         <datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true">
             <converter file="vcf_to_bgzip_converter.xml" target_datatype="bgzip"/>
             <converter file="vcf_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
-            <converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/>    
+            <converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
         </datatype>
         <datatype extension="wsf" type="galaxy.datatypes.wsf:SnpFile" display_in_upload="true"/>
         <datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="false"/>
@@ -274,10 +274,10 @@
     </registration>
     <sniffers>
         <!--
-          The order in which Galaxy attempts to determine data types is 
-          important because some formats are much more loosely defined 
-          than others.  The following list should be the most rigidly 
-          defined format first, followed by next-most rigidly defined, 
+          The order in which Galaxy attempts to determine data types is
+          important because some formats are much more loosely defined
+          than others.  The following list should be the most rigidly
+          defined format first, followed by next-most rigidly defined,
           and so on.
         -->
         <sniffer type="galaxy.datatypes.tabular:Vcf"/>
diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index 670c6fdbd4b..5652df765b7 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -51,7 +51,7 @@
     <tool file="fasta_tools/fasta_to_tabular.xml" />
     <tool file="filters/gff2bed.xml" />
     <tool file="maf/maf_to_bed.xml" />
-    <tool file="maf/maf_to_interval.xml" /> 
+    <tool file="maf/maf_to_interval.xml" />
     <tool file="maf/maf_to_fasta.xml" />
     <tool file="fasta_tools/tabular_to_fasta.xml" />
     <tool file="fastq/fastq_to_fasta.xml" />
@@ -78,13 +78,13 @@
         <tool file="filters/gff/extract_GFF_Features.xml" />
         <tool file="filters/gff/gff_filter_by_attribute.xml" />
         <tool file="filters/gff/gff_filter_by_feature_count.xml" />
-		<tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" />
+        <tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" />
   </section>
   <section name="Join, Subtract and Group" id="group">
     <tool file="filters/joiner.xml" />
     <tool file="filters/compare.xml"/>
     <tool file="new_operations/subtract_query.xml"/>
-    <tool file="stats/grouping.xml" />   
+    <tool file="stats/grouping.xml" />
     <tool file="new_operations/column_join.xml"/>
   </section>
   <section name="Extract Features" id="features">
@@ -112,7 +112,7 @@
     <tool file="extract/phastOdds/phastOdds_tool.xml" />
   </section>
   <section name="Operate on Genomic Intervals" id="bxops">
-    <tool file="new_operations/intersect.xml" />  
+    <tool file="new_operations/intersect.xml" />
     <tool file="new_operations/subtract.xml" />
     <tool file="new_operations/merge.xml" />
     <tool file="new_operations/concat.xml" />
@@ -127,7 +127,7 @@
   </section>
   <section name="Statistics" id="stats">
     <tool file="stats/gsummary.xml" />
-    <tool file="filters/uniq.xml" /> 
+    <tool file="filters/uniq.xml" />
     <tool file="stats/cor.xml" />
     <tool file="stats/generate_matrix_for_pca_lda.xml" />
     <tool file="stats/lda_analy.xml" />
@@ -223,13 +223,13 @@
     <tool file="emboss_5/emboss_chips.xml" />
     <tool file="emboss_5/emboss_cirdna.xml" />
     <tool file="emboss_5/emboss_codcmp.xml" />
-    <tool file="emboss_5/emboss_coderet.xml" /> 
+    <tool file="emboss_5/emboss_coderet.xml" />
     <tool file="emboss_5/emboss_compseq.xml" />
-    <tool file="emboss_5/emboss_cpgplot.xml" /> 
+    <tool file="emboss_5/emboss_cpgplot.xml" />
     <tool file="emboss_5/emboss_cpgreport.xml" />
     <tool file="emboss_5/emboss_cusp.xml" />
     <tool file="emboss_5/emboss_cutseq.xml" />
-    <tool file="emboss_5/emboss_dan.xml" /> 
+    <tool file="emboss_5/emboss_dan.xml" />
     <tool file="emboss_5/emboss_degapseq.xml" />
     <tool file="emboss_5/emboss_descseq.xml" />
     <tool file="emboss_5/emboss_diffseq.xml" />
@@ -245,7 +245,7 @@
     <tool file="emboss_5/emboss_etandem.xml" />
     <tool file="emboss_5/emboss_extractfeat.xml" />
     <tool file="emboss_5/emboss_extractseq.xml" />
-    <tool file="emboss_5/emboss_freak.xml" /> 
+    <tool file="emboss_5/emboss_freak.xml" />
     <tool file="emboss_5/emboss_fuzznuc.xml" />
     <tool file="emboss_5/emboss_fuzzpro.xml" />
     <tool file="emboss_5/emboss_fuzztran.xml" />
@@ -266,7 +266,7 @@
     <tool file="emboss_5/emboss_merger.xml" />
     <tool file="emboss_5/emboss_msbar.xml" />
     <tool file="emboss_5/emboss_needle.xml" />
-    <tool file="emboss_5/emboss_newcpgreport.xml" /> 
+    <tool file="emboss_5/emboss_newcpgreport.xml" />
     <tool file="emboss_5/emboss_newcpgseek.xml" />
     <tool file="emboss_5/emboss_newseq.xml" />
     <tool file="emboss_5/emboss_noreturn.xml" />
@@ -294,7 +294,7 @@
     <tool file="emboss_5/emboss_revseq.xml" />
     <tool file="emboss_5/emboss_seqmatchall.xml" />
     <tool file="emboss_5/emboss_seqret.xml" />
-    <tool file="emboss_5/emboss_showfeat.xml" /> 
+    <tool file="emboss_5/emboss_showfeat.xml" />
     <tool file="emboss_5/emboss_shuffleseq.xml" />
     <tool file="emboss_5/emboss_sigcleave.xml" />
     <tool file="emboss_5/emboss_sirna.xml" />
@@ -316,7 +316,7 @@
     <tool file="emboss_5/emboss_water.xml" />
     <tool file="emboss_5/emboss_wobble.xml" />
     <tool file="emboss_5/emboss_wordcount.xml" />
-    <tool file="emboss_5/emboss_wordmatch.xml" /> 
+    <tool file="emboss_5/emboss_wordmatch.xml" />
   </section>
   <label text="NGS Toolbox Beta" id="ngs" />
   <section name="NGS: QC and manipulation" id="cshl_library_information">
diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index f0352e4b419..1e3d8d3f7fa 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -144,14 +144,14 @@
     <tool file="regVariation/t_test_two_samples.xml" />
     <tool file="regVariation/compute_q_values.xml" />
     <label text="GFF" id="gff" />
-		<tool file="stats/count_gff_features.xml" />
+      <tool file="stats/count_gff_features.xml" />
   </section>
   <!--
   Keep this section commented until all of the tools have functional tests
   <section name="Wavelet Analysis" id="dwt">
     <tool file="discreteWavelet/execute_dwt_IvC_all.xml" />
     <tool file="discreteWavelet/execute_dwt_cor_aVa_perClass.xml" />
-    <tool file="discreteWavelet/execute_dwt_cor_aVb_all.xml" /> 
+    <tool file="discreteWavelet/execute_dwt_cor_aVb_all.xml" />
     <tool file="discreteWavelet/execute_dwt_var_perClass.xml" />
  </section>
  -->
@@ -184,8 +184,8 @@
     <tool file="regVariation/compute_motif_frequencies_for_all_motifs.xml" />
     <tool file="regVariation/categorize_elements_satisfying_criteria.xml" />s
     <tool file="regVariation/draw_stacked_barplots.xml" />
-    <tool file="regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml" />    
-    <tool file="regVariation/microsatellite_birthdeath.xml" />        
+    <tool file="regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml" />
+    <tool file="regVariation/microsatellite_birthdeath.xml" />
   </section>
   <section name="Multiple regression" id="multReg">
     <tool file="regVariation/linear_regression.xml" />
@@ -241,7 +241,7 @@
   </section>
   <section name="NGS: QC and manipulation" id="NGS_QC">
    <label text="FastQC: fastq/sam/bam" id="fastqcsambam" />
-    <tool file="rgenetics/rgFastQC.xml" />         
+    <tool file="rgenetics/rgFastQC.xml" />
    <label text="Illumina fastq" id="illumina" />
     <tool file="fastq/fastq_groomer.xml" />
     <tool file="fastq/fastq_paired_end_splitter.xml" />
@@ -280,21 +280,21 @@
     <tool file="fastx_toolkit/fastx_collapser.xml" />
     <tool file="fastx_toolkit/fastx_renamer.xml" />
     <tool file="fastx_toolkit/fastx_reverse_complement.xml" />
-     <tool file="fastx_toolkit/fastx_trimmer.xml" />  
+     <tool file="fastx_toolkit/fastx_trimmer.xml" />
   </section>
   <section name="NGS: Picard (beta)" id="picard_beta">
     <label text="QC/Metrics for sam/bam" id="qcsambam"/>
     <tool file="picard/picard_BamIndexStats.xml" />
-    <tool file="picard/rgPicardASMetrics.xml" />    
-    <tool file="picard/rgPicardGCBiasMetrics.xml" />     
-    <tool file="picard/rgPicardLibComplexity.xml" />     
+    <tool file="picard/rgPicardASMetrics.xml" />
+    <tool file="picard/rgPicardGCBiasMetrics.xml" />
+    <tool file="picard/rgPicardLibComplexity.xml" />
     <tool file="picard/rgPicardInsertSize.xml" />
     <tool file="picard/rgPicardHsMetrics.xml" />
   <label text="bam/sam Cleaning" id="picard-clean" />
     <tool file="picard/picard_AddOrReplaceReadGroups.xml" />
     <tool file="picard/picard_ReorderSam.xml" />
     <tool file="picard/picard_ReplaceSamHeader.xml" />
-    <tool file="picard/rgPicardFixMate.xml" />          
+    <tool file="picard/rgPicardFixMate.xml" />
     <tool file="picard/rgPicardMarkDups.xml" />
   </section>
   <!--
diff --git a/tool_list.py b/tool_list.py
index a84f924a030..045fc127e95 100644
--- a/tool_list.py
+++ b/tool_list.py
@@ -4,19 +4,19 @@ import os,sys
 onoff = 1
 tool_list = []
 for line in open("tool_conf.xml.sample", "r"):
-   if line.find("<!--") != -1: 
+   if line.find("<!--") != -1:
       onoff = 0
-   if line.find("file") != -1 and onoff==1: 
-      strs = line.split('\"') 
+   if line.find("file") != -1 and onoff==1:
+      strs = line.split('\"')
       tool_list.append(strs[1])
-   if line.find("<section") != -1 and onoff==1: 
+   if line.find("<section") != -1 and onoff==1:
       keys = line.strip().split('\"')
       n = 0
       strtmp = "section::"
-      while n < len(keys) : 
-         if keys[n].find("id") != -1 : strtmp = strtmp + keys[n+1]  
-         if keys[n].find("name") != -1 : strtmp = strtmp + keys[n+1] + "-" 
-	 n = n + 1
+      while n < len(keys) :
+         if keys[n].find("id") != -1 : strtmp = strtmp + keys[n+1]
+         if keys[n].find("name") != -1 : strtmp = strtmp + keys[n+1] + "-"
+         n = n + 1
       tool_list.append(strtmp.replace(' ', '_'))
    if line.find("-->") != -1:
       onoff =1
@@ -26,42 +26,42 @@ name = []
 id = []
 desc = []
 tool_infos = []
-for tool in tool_list : 
-   if tool.find("section")!=-1 : 
+for tool in tool_list :
+   if tool.find("section")!=-1 :
       tool_info = dict()
       tool_info["id"] = tool
       tool_infos.append(tool_info)
-   if os.path.exists("tools/"+tool) : 
-      for line in open("tools/"+tool) : 
-	  if line.find("<tool ") != -1 and line.find("id") != -1 : 
-	     keys = line.strip().split('\"')
-	     n = 0
-	     tool_info = dict()
-	     tool_info["desc"] = ''
-	     while n < len(keys) : 
-	        if keys[n].find("id") != -1 : tool_info["id"] = keys[n+1].replace(' ', '_') 
-	        if keys[n].find("name") != -1 : tool_info["name"] = keys[n+1] 
-	        if keys[n].find("description") != -1 : tool_info["desc"] = keys[n+1] 
-		n = n + 1
-	     tool_infos.append(tool_info)
-	     break
+   if os.path.exists("tools/"+tool) :
+      for line in open("tools/"+tool) :
+         if line.find("<tool ") != -1 and line.find("id") != -1 :
+            keys = line.strip().split('\"')
+            n = 0
+            tool_info = dict()
+            tool_info["desc"] = ''
+            while n < len(keys) :
+               if keys[n].find("id") != -1 : tool_info["id"] = keys[n+1].replace(' ', '_')
+               if keys[n].find("name") != -1 : tool_info["name"] = keys[n+1]
+               if keys[n].find("description") != -1 : tool_info["desc"] = keys[n+1]
+               n = n + 1
+            tool_infos.append(tool_info)
+            break
 
 flag=0
-if len(sys.argv) == 1 : 
-   for tool_info in tool_infos: 
-      if tool_info["id"].find("section") != -1 : 
+if len(sys.argv) == 1 :
+   for tool_info in tool_infos:
+      if tool_info["id"].find("section") != -1 :
          print "==========================================================================================================================================="
          print "%-45s\t%-40s\t%s" % ("id", "name", tool_info["id"])
          print "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -"
       else :
          print "%-45s\t%-40s" % (tool_info["id"], tool_info["name"])
-else: 
-   for tool_info in tool_infos: 
+else:
+   for tool_info in tool_infos:
       if tool_info["id"].find("section") != -1 :
          flag=0
       elif flag==1:
          print " functional.test_toolbox:TestForTool_%s" % tool_info["id"],
-      if tool_info["id"].replace('section::', '')==sys.argv[1]:  
+      if tool_info["id"].replace('section::', '')==sys.argv[1]:
          flag=1
 
 #for key in tool_infos.keys():