diff --git a/tool-data/shared/ucsc/builds.txt b/tool-data/shared/ucsc/builds.txt
index d7ae4762e7e..bf45c97674c 100644
--- a/tool-data/shared/ucsc/builds.txt
+++ b/tool-data/shared/ucsc/builds.txt
@@ -786,6 +786,7 @@ eschColi_K12	Escherichia coli K12 (eschColi_K12)
 aeroHydr_ATCC7966	Aeromonas hydrophila subsp. hydrophila ATCC 7966 (aeroHydr_ATCC7966)
 baciAnth_AMES	Bacillus anthracis str. Ames (baciAnth_AMES)
 shewOnei	Shewanella oneidensis MR-1 (shewOnei)
+equCab2	Horse Sep. 2007 (equCab2)
 arabidopsis	Arabidopsis thaliana TAIR9
 arabidopsis_tair8	Arabidopsis thaliana TAIR8
 araTha1	Arabidopsis thaliana TAIR7
diff --git a/tools/sr_mapping/bowtie_color_wrapper.xml b/tools/sr_mapping/bowtie_color_wrapper.xml
index b515e5072e6..a7d9642805c 100644
--- a/tools/sr_mapping/bowtie_color_wrapper.xml
+++ b/tools/sr_mapping/bowtie_color_wrapper.xml
@@ -210,7 +210,7 @@
           <param name="indexSettings" type="select" label="Choose whether to use Default options for building indices or to Set your own">
             <option value="indexPreSet">Default</option>
             <option value="indexFull">Set your own</option>
-          </param> 
+          </param>
           <when value="indexPreSet" />
           <when value="indexFull">
             <conditional name="autoBehavior">
@@ -259,7 +259,7 @@
         <option value="paired">Paired-end</option>
       </param>
       <when value="single">
-        <param name="sInput1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
+        <param name="sInput1" type="data" format="fastqcssanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
         <conditional name="sParams">
           <param name="sSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
             <option value="preSet">Commonly used</option>
@@ -317,8 +317,8 @@
         </conditional> <!-- csParams -->
       </when> <!-- cSingle -->
       <when value="paired">
-        <param name="pInput1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
-        <param name="pInput2" type="data" format="fastqsanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
+        <param name="pInput1" type="data" format="fastqcssanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
+        <param name="pInput2" type="data" format="fastqcssanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
         <param name="pMaxInsert" type="integer" value="1000" label="Maximum insert size for valid paired-end alignments (-X)" />
         <param name="pMateOrient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand (--fr/--rf/--ff)">
           <option value="ff">FF (for SOLiD)</option>
@@ -401,14 +401,14 @@
     <test>
       <!--
       Bowtie command:
-      bowtie -p 4 -S +sam-nohead -q -C chrM_color test-data/bowtie_in1.fastqsanger > test-data/bowtie_out1.sam
+      bowtie -p 4 -S +sam-nohead -q -C chrM_color test-data/bowtie_in1.fastqcssanger > test-data/bowtie_out1.sam
       -p is the number of threads, which is hardcoded above. You need to replace the + with 2 dashes. 
       chrM_color needs to be the base location/name of the index files.
       -->
       <param name="genomeSource" value="indexed" />
       <param name="index" value="equCab2chrM" />
       <param name="sPaired" value="single" />
-      <param name="sInput1" ftype="fastqsanger" value="bowtie_in1.fastqsanger" />
+      <param name="sInput1" ftype="fastqcssanger" value="bowtie_in1.fastqcssanger" />
       <param name="sSettingsType" value="preSet" />
       <param name="suppressHeader" value="true" />
       <output name="output" ftype="sam" file="bowtie_out1.sam" />
@@ -417,7 +417,7 @@
       <!--
       Bowtie command:
       bowtie-build -f -C test-data/chr_m.fasta chrM_color
-      bowtie -X 1000 +ff -n 2 -e 70 -l 28 -X 250 +pairtries 100 +maxbts 125 -k 1 -C +snpfrac 0.001 +col-keepends -p 4 -S +sam-nohead -q chrM_color -1 test-data/bowtie_in3.fastqsanger -2 test-data/bowtie_in4.fastqsanger > test-data/bowtie_out3.sam
+      bowtie -X 1000 +ff -n 2 -e 70 -l 28 -X 250 +pairtries 100 +maxbts 125 -k 1 -C +snpfrac 0.001 +col-keepends -p 4 -S +sam-nohead -q chrM_color -1 test-data/bowtie_in3.fastqcssanger -2 test-data/bowtie_in4.fastqcssanger > test-data/bowtie_out3.sam
       -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes.
       chrM_base is the index files' location/base name. 
       -->
@@ -425,8 +425,8 @@
       <param name="ownFile" value="chr_m.fasta" />
       <param name="indexSettings" value="indexPreSet" />
       <param name="sPaired" value="paired" />
-      <param name="pInput1" ftype="fastqsanger" value="bowtie_in3.fastqsanger" />
-      <param name="pInput2" ftype="fastqsanger" value="bowtie_in4.fastqsanger" />
+      <param name="pInput1" ftype="fastqcssanger" value="bowtie_in3.fastqcssanger" />
+      <param name="pInput2" ftype="fastqcssanger" value="bowtie_in4.fastqcssanger" />
       <param name="pMaxInsert" value="1000" />
       <param name="pMateOrient" value="ff" />
       <param name="pSettingsType" value="full" />
@@ -460,14 +460,14 @@
     <test>
       <!--
       Bowtie command:
-      bowtie -n 2 -e 70 -l 28 +maxbts 125 -k 1 -C +snpfrac 0.001 +col-keepends -p 4 -S +sam-nohead -q chrM_color test-data/bowtie_in1.fastqsanger > test-data/bowtie_out5.sam
+      bowtie -n 2 -e 70 -l 28 +maxbts 125 -k 1 -C +snpfrac 0.001 +col-keepends -p 4 -S +sam-nohead -q chrM_color test-data/bowtie_in1.fastqcssanger > test-data/bowtie_out5.sam
       -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes.
       chrM_base is the index files' location/base name. 
       -->
       <param name="genomeSource" value="indexed" />
       <param name="index" value="equCab2chrM" />
       <param name="sPaired" value="single" />
-      <param name="sInput1" ftype="fastqsanger" value="bowtie_in1.fastqsanger" />
+      <param name="sInput1" ftype="fastqcssanger" value="bowtie_in1.fastqcssanger" />
       <param name="sSettingsType" value="full" />
       <param name="sSkip" value="0" />
       <param name="sAlignLimit" value="-1" />
@@ -496,7 +496,7 @@
       <!--
       Bowtie command:
       bowtie-build +noauto +bmaxdivn 4 +dcv 1024 +offrate 5 +ftabchars 10 +little -C -f test-data/chr_m.fasta chrM_color
-      bowtie -X 1000 +ff -p 4 -S +sam-nohead -q -C chrM_color -1 test-data/bowtie_in3.fastqsanger -2 test-data/bowtie_in4.fastqsanger > test-data/bowtie_out7.sam
+      bowtie -X 1000 +ff -p 4 -S +sam-nohead -q -C chrM_color -1 test-data/bowtie_in3.fastqcssanger -2 test-data/bowtie_in4.fastqcssanger > test-data/bowtie_out7.sam
       -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes.
       chrM_base is the index files' location/base name. 
       -->
@@ -517,8 +517,8 @@
       <param name="seed" value="-1" />
       <param name="cutoff" value="-1" />
       <param name="sPaired" value="paired" />
-      <param name="pInput1" ftype="fastqsanger" value="bowtie_in3.fastqsanger" />
-      <param name="pInput2" ftype="fastqsanger" value="bowtie_in4.fastqsanger" />
+      <param name="pInput1" ftype="fastqcssanger" value="bowtie_in3.fastqcssanger" />
+      <param name="pInput2" ftype="fastqcssanger" value="bowtie_in4.fastqcssanger" />
       <param name="pMaxInsert" value="1000" />
       <param name="pMateOrient" value="ff" />
       <param name="pSettingsType" value="preSet" />
@@ -558,7 +558,7 @@ Bowtie accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare yo
 The output is in SAM format, and has the following columns::
 
     Column  Description
-  --------  --------------------------------------------------------   
+  --------  --------------------------------------------------------
    1 QNAME  Query (pair) NAME
    2 FLAG   bitwise FLAG
    3 RNAME  Reference sequence NAME
@@ -571,7 +571,7 @@ The output is in SAM format, and has the following columns::
   10 SEQ    query SEQuence on the same strand as the reference
   11 QUAL   query QUALity (ASCII-33 gives the Phred base quality)
   12 OPT    variable OPTional fields in the format TAG:VTYPE:VALUE
-  
+
 The flags are as follows::
 
     Flag  Description