diff --git a/tool_collections/samtools/macros.xml b/tool_collections/samtools/macros.xml
index 75344d32a1d..d56d915d22d 100644
--- a/tool_collections/samtools/macros.xml
+++ b/tool_collections/samtools/macros.xml
@@ -6,13 +6,13 @@
         </requirements>
     </xml>
     <!-- NOTE: for some tools only the version of the requirement but not the
-        tool's version is controlled by the TOOL_VERSION token 
-        (because their version is ahead of the requirement version .. 
+        tool's version is controlled by the TOOL_VERSION token
+        (because their version is ahead of the requirement version ..
          please only bump the minor version in order to let the requirement
          version catch up eventually). To find the tools check:
         `grep "<tool" . -r | grep -v VERSION_SUFFIX | cut -d":" -f 1` -->
     <token name="@TOOL_VERSION@">1.22</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">24.0</token>
     <token name="@FLAGS@"><![CDATA[
         #set $flags = 0
@@ -101,7 +101,7 @@
             #end if
             reffai=\$reffa.fai &&
         #elif $addref_cond.addref_select == "cached":
-            ## in case of cached the absolute path is used which allows to read 
+            ## in case of cached the absolute path is used which allows to read
             ## a cram file  without specifying the reference
             reffa='${addref_cond.ref.fields.path}' &&
             reffai=\$reffa.fai &&
diff --git a/tool_collections/samtools/samtools_ampliconclip/samtools_ampliconclip.xml b/tool_collections/samtools/samtools_ampliconclip/samtools_ampliconclip.xml
index b0209ca9429..eb7cc4d3983 100644
--- a/tool_collections/samtools/samtools_ampliconclip/samtools_ampliconclip.xml
+++ b/tool_collections/samtools/samtools_ampliconclip/samtools_ampliconclip.xml
@@ -8,6 +8,7 @@
     <expand macro="version_command"/>
     <command><![CDATA[
         @ADDTHREADS@
+        @ADDMEMORY@
         samtools ampliconclip
             $hard_clip_mode
             #if $min_length:
@@ -16,8 +17,8 @@
             --tolerance $tolerance
             $strand
             -b '${input_bed}'
-            -u 
-            $both_ends 
+            -u
+            $both_ends
             $no_excluded
             #if $write_primer_counts:
                 --primer-counts '${primer_counts}'
@@ -25,8 +26,8 @@
             -@ \$addthreads
             '${input_bam}'
             | samtools collate -@ \$addthreads -O -u -
-            | samtools fixmate -@ \$addthreads -u - - 
-            | samtools sort -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}" -o '${output_bam}'
+            | samtools fixmate -@ \$addthreads -u - -
+            | samtools sort -@ \$addthreads -m \$addmemory"M" -T "\${TMPDIR:-.}" -o '${output_bam}'
     ]]></command>
     <inputs>
         <param name="input_bed" type="data" format="bed" label="Genetic intervals (in BED format)" />
diff --git a/tool_collections/samtools/samtools_fastx/samtools_fastx.xml b/tool_collections/samtools/samtools_fastx/samtools_fastx.xml
index 65e1b67dad8..56e9ba1366b 100644
--- a/tool_collections/samtools/samtools_fastx/samtools_fastx.xml
+++ b/tool_collections/samtools/samtools_fastx/samtools_fastx.xml
@@ -8,9 +8,10 @@
     <expand macro="version_command" />
     <command><![CDATA[
 @ADDTHREADS@
+@ADDMEMORY@
 ## name sort input file if neccessary
 #if not $input.is_of_type('qname_sorted.bam', 'qname_input_sorted.bam'):
-    samtools sort -@ \$addthreads -n '$input' -T "\${TMPDIR:-.}" > input &&
+    samtools sort -@ \$addthreads -m \$addmemory"M" -n '$input' -T "\${TMPDIR:-.}" > input &&
 #else:
     ln -s '$input' input &&
 #end if
diff --git a/tool_collections/samtools/samtools_fixmate/samtools_fixmate.xml b/tool_collections/samtools/samtools_fixmate/samtools_fixmate.xml
index f9495de19a3..89e8ffa55b9 100644
--- a/tool_collections/samtools/samtools_fixmate/samtools_fixmate.xml
+++ b/tool_collections/samtools/samtools_fixmate/samtools_fixmate.xml
@@ -1,4 +1,4 @@
-<tool id="samtools_fixmate" name="Samtools fixmate" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
+<tool id="samtools_fixmate" name="Samtools fixmate" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@">
     <description>fill mate coordinates, ISIZE and mate related flags</description>
     <macros>
         <import>macros.xml</import>
@@ -8,10 +8,11 @@
     <expand macro="version_command"/>
     <command><![CDATA[
         @ADDTHREADS@
+        @ADDMEMORY@
         ## name sort input
         #if not $bamfile.is_of_type('qname_sorted.bam', 'qnamed_input_sorted.bam'):
             samtools sort
-            -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
+            -@ \$addthreads -m \$addmemory"M" -T "\${TMPDIR:-.}"
             -n
             -O BAM
             -o namesorted.bam
diff --git a/tool_collections/samtools/samtools_markdup/samtools_markdup.xml b/tool_collections/samtools/samtools_markdup/samtools_markdup.xml
index 9968ef1e94d..9a8c7ddc47a 100644
--- a/tool_collections/samtools/samtools_markdup/samtools_markdup.xml
+++ b/tool_collections/samtools/samtools_markdup/samtools_markdup.xml
@@ -1,4 +1,4 @@
-<tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@" >
+<tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@" >
     <description>marks duplicate alignments</description>
     <macros>
         <import>macros.xml</import>
@@ -8,10 +8,11 @@
     <expand macro="version_command"/>
     <command><![CDATA[
 @ADDTHREADS@
+@ADDMEMORY@
 ## coordinate sort input
 #if not $bamfile.is_of_type('bam'):
     samtools sort
-    -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
+    -@ \$addthreads -m \$addmemory"M" -T "\${TMPDIR:-.}"
     -O sam
     -o coordsort.sam
     '$bamfile' &&
diff --git a/tool_collections/samtools/samtools_merge/samtools_merge.xml b/tool_collections/samtools/samtools_merge/samtools_merge.xml
index 2980cf1cbdd..38893695823 100644
--- a/tool_collections/samtools/samtools_merge/samtools_merge.xml
+++ b/tool_collections/samtools/samtools_merge/samtools_merge.xml
@@ -8,13 +8,14 @@
     <expand macro="version_command"/>
     <command><![CDATA[
 @ADDTHREADS@
+@ADDMEMORY@
 ## prepare input (sort sam, link other), determine input ordering
 ## and check for consistent input ordering
 #set sortby=''
 #for $i, $bam in enumerate( $bamfiles ):
     #if $bam.is_of_type('sam', 'cram', ):
         samtools sort
-        -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
+        -@ \$addthreads -m \$addmemory"M" -T "\${TMPDIR:-.}"
         -O sam
         -o ${i}.sam
         '$bam' &&
diff --git a/tool_collections/samtools/samtools_slice_bam/samtools_slice_bam.xml b/tool_collections/samtools/samtools_slice_bam/samtools_slice_bam.xml
index c0bf4338550..19c52c46b64 100644
--- a/tool_collections/samtools/samtools_slice_bam/samtools_slice_bam.xml
+++ b/tool_collections/samtools/samtools_slice_bam/samtools_slice_bam.xml
@@ -1,4 +1,4 @@
-<tool id="samtools_slice_bam" name="Slice" version="2.0.6" profile="@PROFILE@">
+<tool id="samtools_slice_bam" name="Slice" version="2.0.7" profile="@PROFILE@">
     <description>BAM by genomic regions</description>
     <macros>
         <import>macros.xml</import>
@@ -9,16 +9,18 @@
     <expand macro="version_command"/>
 
     <command><![CDATA[
+    @ADDTHREADS@
+    @ADDMEMORY@
     ln -s '${input_bam}' temp_input.bam &&
     ln -s '${input_bam.metadata.bam_index}' temp_input.bam.bai &&
 
     #if str($slice_method.slice_method_selector) == "bed":
-        samtools view -@ \${GALAXY_SLOTS:-1} -b -L "${input_interval}" -o unsorted_output.bam temp_input.bam &&
+        samtools view -@ \$addthreads -b -L "${input_interval}" -o unsorted_output.bam temp_input.bam &&
     #elif str($slice_method.slice_method_selector) == "chr":
-        samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam
+        samtools view -@ \$addthreads -b -o unsorted_output.bam temp_input.bam
         ${ ' '.join( map( lambda x:'"%s"' % ( x ), str( $slice_method.refs ).split(",") ) ) } &&
     #elif str($slice_method.slice_method_selector) == "man":
-        samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam
+        samtools view -@ \$addthreads -b -o unsorted_output.bam temp_input.bam
 
         #for $region in $slice_method.regions:
             "${region.chrom}:${region.start}-${region.end}"
@@ -29,7 +31,8 @@
     samtools sort
         -O bam
         -T "\${TMPDIR:-.}"
-        -@ \${GALAXY_SLOTS:-1}
+        -@ \$addthreads
+        -m \$addmemory"M"
         -o '${output_bam}'
         unsorted_output.bam
     ]]></command>
diff --git a/tool_collections/samtools/samtools_sort/samtools_sort.xml b/tool_collections/samtools/samtools_sort/samtools_sort.xml
index d249e5b969e..042229f6bc7 100644
--- a/tool_collections/samtools/samtools_sort/samtools_sort.xml
+++ b/tool_collections/samtools/samtools_sort/samtools_sort.xml
@@ -8,7 +8,7 @@
     <expand macro="version_command"/>
     <command><![CDATA[
         @ADDTHREADS@
-	@ADDMEMORY@
+        @ADDMEMORY@
         samtools sort
             -@ \$addthreads
             -m \$addmemory"M"