diff --git a/tools/samtools/bam_to_sam.xml b/tools/samtools/bam_to_sam.xml
index 0fdb3acd267..632c2977afe 100644
--- a/tools/samtools/bam_to_sam.xml
+++ b/tools/samtools/bam_to_sam.xml
@@ -1,4 +1,4 @@
-<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.0">
+<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.1">
   <requirements>
     <requirement type="package">samtools</requirement>
   </requirements>
@@ -12,7 +12,7 @@
     <param name="input1" type="data" format="bam" label="BAM File to Convert" />
   </inputs>
   <outputs>
-    <data name="output1" format="sam" label="Converted SAM" />
+    <data format="sam" name="output1" label="${tool.name} on ${on_string}: converted SAM" />
   </outputs>
   <tests>
     <test>
diff --git a/tools/samtools/sam_merge.xml b/tools/samtools/sam_merge.xml
index 75e420eaed1..9613c7fab9f 100644
--- a/tools/samtools/sam_merge.xml
+++ b/tools/samtools/sam_merge.xml
@@ -1,4 +1,4 @@
-<tool id="sam_merge" name="Merge BAM Files" version="1.1.0">
+<tool id="sam_merge" name="Merge BAM Files" version="1.1.1">
   <description>merges BAM files together</description>
   <requirements>
     <requirement type="package">samtools</requirement>
@@ -20,7 +20,7 @@
     </repeat>
   </inputs>
   <outputs>
-    <data name="output1" format="bam" label="Merged BAM" />
+    <data format="bam" name="output1" label="${tool.name} on ${on_string}: merged BAM" />
   </outputs>
   <tests>
     <!-- TODO: add ability to test framework to test without at least 
diff --git a/tools/samtools/sam_pileup.xml b/tools/samtools/sam_pileup.xml
index f1e6061b622..430582962bf 100644
--- a/tools/samtools/sam_pileup.xml
+++ b/tools/samtools/sam_pileup.xml
@@ -1,4 +1,4 @@
-<tool id="sam_pileup" name="Generate pileup" version="1.1.0">
+<tool id="sam_pileup" name="Generate pileup" version="1.1.1">
   <description>from BAM dataset</description>
   <requirements>
     <requirement type="package">samtools</requirement>
@@ -73,7 +73,7 @@
     </conditional>
   </inputs>
   <outputs>
-    <data format="tabular" name="output1" label="Converted Pileup" />
+    <data format="tabular" name="output1" label="${tool.name} on ${on_string}: converted pileup" />
   </outputs>
   <tests>
     <test>
diff --git a/tools/samtools/sam_to_bam.xml b/tools/samtools/sam_to_bam.xml
index cc4d81d6b3b..f9d6fb6fabb 100644
--- a/tools/samtools/sam_to_bam.xml
+++ b/tools/samtools/sam_to_bam.xml
@@ -1,4 +1,4 @@
-<tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.0">
+<tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.1">
   <description>converts SAM format to BAM format</description>
   <requirements>
     <requirement type="package">samtools</requirement>
@@ -34,7 +34,7 @@
     </conditional>
   </inputs>
   <outputs>
-    <data name="output1" format="bam" label="Converted BAM" />
+    <data format="bam" name="output1" label="${tool.name} on ${on_string}: converted BAM" />
   </outputs>
   <tests>
     <test>
diff --git a/tools/sr_mapping/PerM.xml b/tools/sr_mapping/PerM.xml
index 25ba89e2bff..cc290c90f97 100644
--- a/tools/sr_mapping/PerM.xml
+++ b/tools/sr_mapping/PerM.xml
@@ -1,4 +1,4 @@
-<tool id="PerM" name="Map with PerM" version="1.1.1">
+<tool id="PerM" name="Map with PerM" version="1.1.2">
   <description>for SOLiD and Illumina</description>
   <!-- works with PerM version 0.2.6 -->
   <requirements>
@@ -159,11 +159,11 @@
     </param>
   </inputs>
   <outputs>
-    <data name="output" format="sam" label="Mapped Reads" /> 
-    <data name="unmappedReadOut" format="fastqsanger" label="Unmapped Reads">
+    <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads" />
+    <data format="fastqsanger" name="unmappedReadOut" label="${tool.name} on ${on_string}: unmapped reads">
       <filter>bUnmappedRead == "true" and s["space"] == "base"</filter>
     </data>
-    <data name="unmappedReadOutCS" format="fastqcssanger" label="Unmapped Reads">
+    <data format="fastqcssanger" name="unmappedReadOutCS" label="${tool.name} on ${on_string}: unmapped reads">
       <filter>bUnmappedRead == "true" and s["space"] == "color"</filter>
     </data>
   </outputs>
diff --git a/tools/sr_mapping/bowtie_color_wrapper.xml b/tools/sr_mapping/bowtie_color_wrapper.xml
index 00fe1969a97..d332bd98869 100644
--- a/tools/sr_mapping/bowtie_color_wrapper.xml
+++ b/tools/sr_mapping/bowtie_color_wrapper.xml
@@ -1,4 +1,4 @@
-<tool id="bowtie_color_wrapper" name="Map with Bowtie for SOLiD" version="1.1.0">
+<tool id="bowtie_color_wrapper" name="Map with Bowtie for SOLiD" version="1.1.1">
   <requirements><requirement type='package'>bowtie</requirement></requirements>
   <description></description>
   <command interpreter="python">
@@ -336,7 +336,7 @@
     <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information by default" />
   </inputs>
   <outputs>
-    <data format="sam" name="output" label="Mapped Reads">
+    <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
       <actions>
         <conditional name="refGenomeSource.genomeSource">
           <when value="indexed">
@@ -350,7 +350,7 @@
         </conditional>
       </actions>
     </data>
-    <data format="fastqcssanger" name="output_suppressed_reads_l" label="Suppressed Reads">
+    <data format="fastqcssanger" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
       <filter>((
           singlePaired['sPaired'] == "single" and
           singlePaired['sParams']['sSettingsType'] == "full" and
@@ -362,12 +362,12 @@
         ))
       </filter>
     </data>
-    <data format="fastqcssanger" name="output_suppressed_reads_r" label="Suppressed Reads (R)">
+    <data format="fastqcssanger" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
       <filter>singlePaired['sPaired'] == "paired"</filter>
       <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
       <filter>singlePaired['pParams']['pMaxFile'] is True</filter>
     </data>
-    <data format="fastqcssanger" name="output_unmapped_reads_l" label="Unmapped Reads (L)">
+    <data format="fastqcssanger" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
       <filter>
         ((
           singlePaired['sPaired'] == "single" and
@@ -380,7 +380,7 @@
         ))
       </filter>
     </data>
-    <data format="fastqcssanger" name="output_unmapped_reads_r" label="Unmapped Reads (R)">
+    <data format="fastqcssanger" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
       <filter>singlePaired['sPaired'] == "paired"</filter>
       <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
       <filter>singlePaired['pParams']['pUnmappedFile'] is True</filter>
diff --git a/tools/sr_mapping/bowtie_wrapper.xml b/tools/sr_mapping/bowtie_wrapper.xml
index cae31ddf104..81d62886bee 100644
--- a/tools/sr_mapping/bowtie_wrapper.xml
+++ b/tools/sr_mapping/bowtie_wrapper.xml
@@ -1,4 +1,4 @@
-<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.0">
+<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.1">
   <requirements><requirement type='package'>bowtie</requirement></requirements>
   <description></description>
   <parallelism method="basic"></parallelism>
@@ -319,7 +319,7 @@
     <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information by default" />
   </inputs>
   <outputs>
-    <data format="sam" name="output" label="Mapped Reads">
+    <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
       <actions>
         <conditional name="refGenomeSource.genomeSource">
           <when value="indexed">
@@ -333,7 +333,7 @@
         </conditional>
       </actions>
     </data>
-    <data format="fastqsanger" name="output_suppressed_reads_l" label="Suppressed Reads">
+    <data format="fastqsanger" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
       <filter>((
           singlePaired['sPaired'] == "single" and
           singlePaired['sParams']['sSettingsType'] == "full" and
@@ -345,12 +345,12 @@
         ))
       </filter>
     </data>
-    <data format="fastqsanger" name="output_suppressed_reads_r" label="Suppressed Reads (R)">
+    <data format="fastqsanger" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
       <filter>singlePaired['sPaired'] == "paired"</filter>
       <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
       <filter>singlePaired['pParams']['pMaxFile'] is True</filter>
     </data>
-    <data format="fastqsanger" name="output_unmapped_reads_l" label="Unmapped Reads (L)">
+    <data format="fastqsanger" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
       <filter>
         ((
           singlePaired['sPaired'] == "single" and
@@ -363,7 +363,7 @@
         ))
       </filter>
     </data>
-    <data format="fastqsanger" name="output_unmapped_reads_r" label="Unmapped Reads (R)">
+    <data format="fastqsanger" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
       <filter>singlePaired['sPaired'] == "paired"</filter>
       <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
       <filter>singlePaired['pParams']['pUnmappedFile'] is True</filter>
diff --git a/tools/sr_mapping/bwa_wrapper.xml b/tools/sr_mapping/bwa_wrapper.xml
index 6f4ed648328..a42cd18a7c2 100644
--- a/tools/sr_mapping/bwa_wrapper.xml
+++ b/tools/sr_mapping/bwa_wrapper.xml
@@ -1,4 +1,4 @@
-<tool id="bwa_wrapper" name="Map with BWA" version="1.2.0">
+<tool id="bwa_wrapper" name="Map with BWA" version="1.2.1">
   <description></description>
   <parallelism method="basic"></parallelism>
   <command interpreter="python">
@@ -113,7 +113,7 @@
     <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Suppress the header in the output SAM file" help="BWA produces SAM with several lines of header information" />
   </inputs>
   <outputs>
-    <data format="sam" name="output" label="Mapped Reads">
+    <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
       <actions>
         <conditional name="genomeSource.refGenomeSource">
           <when value="indexed">
diff --git a/tools/sr_mapping/lastz_paired_reads_wrapper.xml b/tools/sr_mapping/lastz_paired_reads_wrapper.xml
index e8f1ca1dc5e..9f9f0f1c9d9 100644
--- a/tools/sr_mapping/lastz_paired_reads_wrapper.xml
+++ b/tools/sr_mapping/lastz_paired_reads_wrapper.xml
@@ -1,4 +1,4 @@
-<tool id="lastz_paired_reads_wrapper" name="Lastz paired reads" version="1.1.0">
+<tool id="lastz_paired_reads_wrapper" name="Lastz paired reads" version="1.1.1">
     <description> map short paired reads against reference sequence</description>
     <command interpreter="python">lastz_paired_reads_wrapper.py
       #if $seq_name.how_to_name=="yes":
@@ -47,7 +47,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="sam" name="output1" label="Mapped Reads" />
+        <data format="sam" name="output1" label="${tool.name} on ${on_string}: mapped reads" />
     </outputs>
     <requirements>
         <requirement type="package">lastz</requirement>
diff --git a/tools/sr_mapping/lastz_wrapper.xml b/tools/sr_mapping/lastz_wrapper.xml
index 0fc13212772..dbec0550096 100644
--- a/tools/sr_mapping/lastz_wrapper.xml
+++ b/tools/sr_mapping/lastz_wrapper.xml
@@ -1,4 +1,4 @@
-<tool id="lastz_wrapper_2" name="Lastz" version="1.2.1">
+<tool id="lastz_wrapper_2" name="Lastz" version="1.2.2">
     <description> map short reads against reference sequence</description>
     <command interpreter="python">lastz_wrapper.py
       #if $seq_name.how_to_name=="yes":
@@ -129,7 +129,7 @@
         </param>
     </inputs>
     <outputs>
-        <data format="tabular" name="output1" label="Mapped Reads">
+        <data format="tabular" name="output1" label="${tool.name} on ${on_string}: mapped reads">
             <change_format>
                 <when input="out_format" value="sam" format="sam" />
             </change_format>
diff --git a/tools/sr_mapping/srma_wrapper.xml b/tools/sr_mapping/srma_wrapper.xml
index 02c348f0d35..75c3f0c36b4 100644
--- a/tools/sr_mapping/srma_wrapper.xml
+++ b/tools/sr_mapping/srma_wrapper.xml
@@ -1,4 +1,4 @@
-<tool id="srma_wrapper" name="Re-align with SRMA" version="0.2.0">
+<tool id="srma_wrapper" name="Re-align with SRMA" version="0.2.1">
   <description></description>
   <command interpreter="python">srma_wrapper.py 
     #if $refGenomeSource.refGenomeSource_type == "history":
@@ -61,7 +61,7 @@
     </conditional>
   </inputs>
   <outputs>
-    <data format="bam" name="output" label="Re-aligned Reads">
+    <data format="bam" name="output" label="${tool.name} on ${on_string}: re-aligned reads">
       <actions>
         <conditional name="refGenomeSource.refGenomeSource_type">
           <when value="built-in">