diff --git a/test-data/sam_to_bam_out1.bam b/test-data/sam_to_bam_out1.bam
deleted file mode 100644
index 95c65de8572..00000000000
Binary files a/test-data/sam_to_bam_out1.bam and /dev/null differ
diff --git a/tools/samtools/sam_merge.xml b/tools/samtools/sam_merge.xml
index b18dd681291..a0aeab23dbf 100644
--- a/tools/samtools/sam_merge.xml
+++ b/tools/samtools/sam_merge.xml
@@ -1,4 +1,4 @@
-<tool id="sam_merge" name="Merge BAM Files" version="1.0.0">
+<tool id="sam_merge" name="Merge BAM Files" version="1.1.0">
   <description>merges BAM files together</description>
   <command interpreter="python">
    sam_merge.py 
diff --git a/tools/samtools/sam_pileup.xml b/tools/samtools/sam_pileup.xml
index f2a8362f215..be296f2b525 100644
--- a/tools/samtools/sam_pileup.xml
+++ b/tools/samtools/sam_pileup.xml
@@ -1,4 +1,4 @@
-<tool id="sam_pileup" name="Generate pileup" version="1.0.0">
+<tool id="sam_pileup" name="Generate pileup" version="1.1.0">
   <description>from BAM dataset</description>
   <command interpreter="python">
     sam_pileup.py
diff --git a/tools/samtools/sam_to_bam.xml b/tools/samtools/sam_to_bam.xml
index 024b880e2dd..1bdbcd61ae0 100644
--- a/tools/samtools/sam_to_bam.xml
+++ b/tools/samtools/sam_to_bam.xml
@@ -1,4 +1,4 @@
-<tool id="sam_to_bam" name="SAM-to-BAM" version="1.0.0">
+<tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.0">
   <description>converts SAM format to BAM format</description>
   <command interpreter="python">
 sam_to_bam.py --input1=$source.input1 --dbkey=${input1.metadata.dbkey} 
diff --git a/tools/sr_mapping/bowtie_color_wrapper.xml b/tools/sr_mapping/bowtie_color_wrapper.xml
index 5974f41bf2b..b515e5072e6 100644
--- a/tools/sr_mapping/bowtie_color_wrapper.xml
+++ b/tools/sr_mapping/bowtie_color_wrapper.xml
@@ -197,12 +197,12 @@
         <option value="history">Use one from the history</option>
       </param>
       <when value="indexed">
-  	    <param name="index" type="select" label="Select the reference genome" help="if your genome of interest is not listed - contact Galaxy team">
-  	      <options from_file="bowtie_indices_color.loc">
-  	        <column name="value" index="1" />
-  	        <column name="name" index="0" />
-  	      </options>
-  	    </param>
+        <param name="index" type="select" label="Select the reference genome" help="if your genome of interest is not listed - contact Galaxy team">
+          <options from_file="bowtie_indices_color.loc">
+            <column name="value" index="1" />
+            <column name="name" index="0" />
+          </options>
+        </param>
       </when>
       <when value="history">
         <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
@@ -252,7 +252,7 @@
           </when>  <!-- cIndexFull -->
         </conditional>  <!-- cIndexParams -->
       </when>  <!-- cHistory -->
- 	</conditional>  <!-- cRefGenomeSource -->
+    </conditional>  <!-- cRefGenomeSource -->
     <conditional name="singlePaired">
       <param name="sPaired" type="select" label="Is this library mate-paired?">
         <option value="single">Single-end</option>
@@ -262,9 +262,9 @@
         <param name="sInput1" type="data" format="fastqsanger" 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>
-   	        <option value="full">Full parameter list</option>
-	      </param>
+            <option value="preSet">Commonly used</option>
+            <option value="full">Full parameter list</option>
+          </param>
           <when value="preSet" />
           <when value="full">
             <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" />  
@@ -327,9 +327,9 @@
         </param>
         <conditional name="pParams">
           <param name="pSettingsType" 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>
-   		    <option value="full">Full parameter list</option>
-	      </param>
+            <option value="preSet">Commonly used</option>
+            <option value="full">Full parameter list</option>
+          </param>
           <when value="preSet" />
           <when value="full">
             <param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" />  
@@ -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 +ff +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.fastqsanger -2 test-data/bowtie_in4.fastqsanger > 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. 
       -->
@@ -533,8 +533,6 @@
 
 Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.
 
-This tool uses Bowtie version 0.12.1.
-
 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
 
 ------
diff --git a/tools/sr_mapping/bowtie_wrapper.xml b/tools/sr_mapping/bowtie_wrapper.xml
index d2c23e6f0f1..eb3bb78c737 100644
--- a/tools/sr_mapping/bowtie_wrapper.xml
+++ b/tools/sr_mapping/bowtie_wrapper.xml
@@ -191,13 +191,13 @@
         <option value="history">Use one from the history</option>
       </param>
       <when value="indexed">
-    	<param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
-  	      <options from_file="bowtie_indices.loc">
-  	        <column name="value" index="1" />
-  	        <column name="name" index="0" />
-  	      </options>
-  	    </param>
-  	  </when>
+        <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
+          <options from_file="bowtie_indices.loc">
+            <column name="value" index="1" />
+            <column name="name" index="0" />
+          </options>
+        </param>
+      </when>
       <when value="history">
         <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
         <conditional name="indexParams">
@@ -246,7 +246,7 @@
           </when>  <!-- indexFull -->
         </conditional>  <!-- indexParams -->
       </when>  <!-- history -->
- 	</conditional>  <!-- refGenomeSource -->
+    </conditional>  <!-- refGenomeSource -->
     <conditional name="singlePaired">
       <param name="sPaired" type="select" label="Is this library mate-paired?">
         <option value="single">Single-end</option>
@@ -256,9 +256,9 @@
         <param name="sInput1" type="data" format="fastqsanger" 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>
-   		    <option value="full">Full parameter list</option>
-	      </param>
+            <option value="preSet">Commonly used</option>
+            <option value="full">Full parameter list</option>
+            </param>
           <when value="preSet" />
           <when value="full">
             <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" />  
@@ -315,9 +315,9 @@
         </param>
         <conditional name="pParams">
           <param name="pSettingsType" 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>
-   		    <option value="full">Full parameter list</option>
-	      </param>
+            <option value="preSet">Commonly used</option>
+            <option value="full">Full parameter list</option>
+          </param>
           <when value="preSet" />
           <when value="full">
             <param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" />  
@@ -506,8 +506,6 @@
 
 Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.
 
-This tool uses Bowtie version 0.12.1.
-
 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
 
 ------
diff --git a/tools/sr_mapping/bwa_wrapper.xml b/tools/sr_mapping/bwa_wrapper.xml
index d90e34916de..20cba4a5066 100644
--- a/tools/sr_mapping/bwa_wrapper.xml
+++ b/tools/sr_mapping/bwa_wrapper.xml
@@ -181,8 +181,6 @@
 
 BWA is a fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (large), such as the human reference genome. It is developed by Heng Li at the Sanger Insitute. Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-60. 
 
-This tool uses BWA version 0.5.5.
-
 ------
 
 **Know what you are doing**