diff --git a/tools/rsem/macros.xml b/tools/rsem/macros.xml
index e68de0558..77f5f291e 100644
--- a/tools/rsem/macros.xml
+++ b/tools/rsem/macros.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
   <macros>
-    <token name="@WRAPPER_VERSION@">1.0.1</token>
+    <token name="@WRAPPER_VERSION@">1.0.2</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="1.3.0=pl526r341h4f16992_4">rsem</requirement>
diff --git a/tools/rsem/rsem.xml b/tools/rsem/rsem.xml
index 144443572..b2328fafb 100644
--- a/tools/rsem/rsem.xml
+++ b/tools/rsem/rsem.xml
@@ -1,5 +1,5 @@
-<tool id="rsembowtie" name="RSEM-Bowtie" version="@WRAPPER_VERSION@">
-  <description></description>
+<tool id="rsem" name="RSEM" version="@WRAPPER_VERSION@">
+  <description>quantification of gene and isoform expression from RNA-Seq data</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -26,7 +26,7 @@
       #if $job.transcript_to_gene_map:
         --transcript-to-gene-map $job.transcript_to_gene_map
       #end if
-      --bowtie
+      $aligner_tool
       #if $job.self_reference.ref_type == 'transcripts':
         $job.self_reference.reference_fasta_file
       #else:
@@ -158,6 +158,12 @@
   ]]></command>
 
   <inputs>
+    <param name="aligner_tool" type="select" label="Aligner tool to use" help="TODO">
+        <option value="--bowtie">Bowtie</option>  
+        <option value="--bowtie2">Bowtie2</option>
+        <option value="--hisat2-hca">HISAT2</option>
+        <option value="--star">RNASTAR</option>
+    </param>
     <conditional name="job">
       <param name="select_job" type="select" label="rsem reference">
         <option value="index">Build rsem reference</option>
diff --git a/tools/rsem/test-data/purged.gtf.log b/tools/rsem/test-data/purged.gtf.log
index 4c16449c1..5882df057 100644
--- a/tools/rsem/test-data/purged.gtf.log
+++ b/tools/rsem/test-data/purged.gtf.log
@@ -1,62 +1,62 @@
-NM_001145149.2"; transcript_id "NM_001145149.2"; 	chrY,chrX
+NM_006883.2"; transcript_id "NM_006883.2"; 	chrY,chrX
+NM_004192.3"; transcript_id "NM_004192.3"; 	chrY,chrX
+NM_001173474.1"; transcript_id "NM_001173474.1"; 	chrY,chrX
+NM_001173473.1"; transcript_id "NM_001173473.1"; 	chrY,chrX
+NM_145177.2"; transcript_id "NM_145177.2"; 	chrY,chrX
+NM_001171135.1"; transcript_id "NM_001171135.1"; 	chrY,chrX
+NM_001171136.1"; transcript_id "NM_001171136.1"; 	chrY,chrX
+NM_004729.3"; transcript_id "NM_004729.3"; 	chrY,chrX
+NR_033381.1"; transcript_id "NR_033381.1"; 	chrY,chrX
+NR_033380.1"; transcript_id "NR_033380.1"; 	chrY,chrX
+NM_001304990.1"; transcript_id "NM_001304990.1"; 	chrY,chrX
+NR_028057.1"; transcript_id "NR_028057.1"; 	chrY,chrX
+NM_018390.3"; transcript_id "NM_018390.3"; 	chrY,chrX
+NM_012227.3"; transcript_id "NM_012227.3"; 	chrY,chrX
+NR_027231.1"; transcript_id "NR_027231.1"; 	chrY,chrX
 NR_027232.1"; transcript_id "NR_027232.1"; 	chrY,chrX
-NM_172247.2"; transcript_id "NM_172247.2"; 	chrY,chrX
-NR_037461.1"; transcript_id "NR_037461.1"; 	chrY,chrX
+NM_013239.4"; transcript_id "NM_013239.4"; 	chrY,chrX
+NM_000451.3"; transcript_id "NM_000451.3"; 	chrY,chrX
+NM_022148.3"; transcript_id "NM_022148.3"; 	chrY,chrX
+NR_110830.1"; transcript_id "NR_110830.1"; 	chrY,chrX
+NM_001012288.2"; transcript_id "NM_001012288.2"; 	chrY,chrX
 NM_001161531.1"; transcript_id "NM_001161531.1"; 	chrY,chrX
-NR_027760.1"; transcript_id "NR_027760.1"; 	chrY,chrX
-NR_033714.1"; transcript_id "NR_033714.1"; 	chrY,chrX
-NM_004043.2"; transcript_id "NM_004043.2"; 	chrY,chrX
-NM_001171135.1"; transcript_id "NM_001171135.1"; 	chrY,chrX
-NM_172249.2"; transcript_id "NM_172249.2"; 	chrY,chrX
-NR_033715.1"; transcript_id "NR_033715.1"; 	chrY,chrX
+NM_001161532.1"; transcript_id "NM_001161532.1"; 	chrY,chrX
 NM_172245.2"; transcript_id "NM_172245.2"; 	chrY,chrX
-NM_001267713.1"; transcript_id "NM_001267713.1"; 	chrY,chrX
-NM_001171039.1"; transcript_id "NM_001171039.1"; 	chrY,chrX
+NM_001161529.1"; transcript_id "NM_001161529.1"; 	chrY,chrX
+NM_172249.2"; transcript_id "NM_172249.2"; 	chrY,chrX
+NR_027760.1"; transcript_id "NR_027760.1"; 	chrY,chrX
 NM_172246.2"; transcript_id "NM_172246.2"; 	chrY,chrX
-NR_033380.1"; transcript_id "NR_033380.1"; 	chrY,chrX
-NM_001321368.1"; transcript_id "NM_001321368.1"; 	chrY,chrX
-NM_001173474.1"; transcript_id "NM_001173474.1"; 	chrY,chrX
-NM_001012288.2"; transcript_id "NM_001012288.2"; 	chrY,chrX
-NM_001321370.1"; transcript_id "NM_001321370.1"; 	chrY,chrX
-NR_135623.1"; transcript_id "NR_135623.1"; 	chrY,chrX
-NM_022148.3"; transcript_id "NM_022148.3"; 	chrY,chrX
-NM_012227.3"; transcript_id "NM_012227.3"; 	chrY,chrX
-NM_005638.5"; transcript_id "NM_005638.5"; 	chrY,chrX
-NM_001171038.1"; transcript_id "NM_001171038.1"; 	chrY,chrX
-NM_005088.2"; transcript_id "NM_005088.2"; 	chrY,chrX
-NM_001173473.1"; transcript_id "NM_001173473.1"; 	chrY,chrX
-NM_001636.3"; transcript_id "NM_001636.3"; 	chrY,chrX
 NM_006140.4"; transcript_id "NM_006140.4"; 	chrY,chrX
+NM_172247.2"; transcript_id "NM_172247.2"; 	chrY,chrX
+NM_001161530.1"; transcript_id "NM_001161530.1"; 	chrY,chrX
+NR_037461.1"; transcript_id "NR_037461.1"; 	chrY,chrX
+NM_001267713.1"; transcript_id "NM_001267713.1"; 	chrY,chrX
 NM_002183.3"; transcript_id "NM_002183.3"; 	chrY,chrX
-NR_037842.1"; transcript_id "NR_037842.1"; 	chrY,chrX
-NM_006883.2"; transcript_id "NM_006883.2"; 	chrY,chrX
-NM_004192.3"; transcript_id "NM_004192.3"; 	chrY,chrX
-NR_106737.1"; transcript_id "NR_106737.1"; 	chrY,chrX
-NR_026710.1"; transcript_id "NR_026710.1"; 	chrY,chrX
-NM_001161532.1"; transcript_id "NM_001161532.1"; 	chrY,chrX
-NM_002414.4"; transcript_id "NM_002414.4"; 	chrY,chrX
-NM_145177.2"; transcript_id "NM_145177.2"; 	chrY,chrX
+NM_001636.3"; transcript_id "NM_001636.3"; 	chrY,chrX
 NR_130733.1"; transcript_id "NR_130733.1"; 	chrY,chrX
-NR_110561.1"; transcript_id "NR_110561.1"; 	chrY,chrX
-NM_176786.1"; transcript_id "NM_176786.1"; 	chrY,chrX
-NR_033381.1"; transcript_id "NR_033381.1"; 	chrY,chrX
-NR_027231.1"; transcript_id "NR_027231.1"; 	chrY,chrX
-NM_001161529.1"; transcript_id "NM_001161529.1"; 	chrY,chrX
-NM_000451.3"; transcript_id "NM_000451.3"; 	chrY,chrX
-NM_004729.3"; transcript_id "NM_004729.3"; 	chrY,chrX
-NM_013239.4"; transcript_id "NM_013239.4"; 	chrY,chrX
+NR_026710.1"; transcript_id "NR_026710.1"; 	chrY,chrX
 NR_026711.1"; transcript_id "NR_026711.1"; 	chrY,chrX
-NM_001161530.1"; transcript_id "NM_001161530.1"; 	chrY,chrX
-NR_027383.1"; transcript_id "NR_027383.1"; 	chrY,chrX
-NR_028057.1"; transcript_id "NR_028057.1"; 	chrY,chrX
-NR_110830.1"; transcript_id "NR_110830.1"; 	chrY,chrX
-NM_002186.2"; transcript_id "NM_002186.2"; 	chrY,chrX
-NM_001122898.2"; transcript_id "NM_001122898.2"; 	chrY,chrX
 NM_178129.4"; transcript_id "NM_178129.4"; 	chrY,chrX
-NM_001185183.1"; transcript_id "NM_001185183.1"; 	chrY,chrX
-NM_001321369.1"; transcript_id "NM_001321369.1"; 	chrY,chrX
-NM_018390.3"; transcript_id "NM_018390.3"; 	chrY,chrX
-NM_001304990.1"; transcript_id "NM_001304990.1"; 	chrY,chrX
+NR_027383.1"; transcript_id "NR_027383.1"; 	chrY,chrX
+NM_005088.2"; transcript_id "NM_005088.2"; 	chrY,chrX
+NM_004043.2"; transcript_id "NM_004043.2"; 	chrY,chrX
+NM_001171038.1"; transcript_id "NM_001171038.1"; 	chrY,chrX
+NM_001171039.1"; transcript_id "NM_001171039.1"; 	chrY,chrX
+NR_106737.1"; transcript_id "NR_106737.1"; 	chrY,chrX
+NR_037842.1"; transcript_id "NR_037842.1"; 	chrY,chrX
 NM_001321367.1"; transcript_id "NM_001321367.1"; 	chrY,chrX
+NM_001321369.1"; transcript_id "NM_001321369.1"; 	chrY,chrX
+NM_001122898.2"; transcript_id "NM_001122898.2"; 	chrY,chrX
+NM_001321370.1"; transcript_id "NM_001321370.1"; 	chrY,chrX
+NM_001321368.1"; transcript_id "NM_001321368.1"; 	chrY,chrX
+NM_002414.4"; transcript_id "NM_002414.4"; 	chrY,chrX
+NR_135623.1"; transcript_id "NR_135623.1"; 	chrY,chrX
 NM_005840.2"; transcript_id "NM_005840.2"; 	chrY,chrX
-NM_001171136.1"; transcript_id "NM_001171136.1"; 	chrY,chrX
+NM_001145149.2"; transcript_id "NM_001145149.2"; 	chrY,chrX
+NR_033715.1"; transcript_id "NR_033715.1"; 	chrY,chrX
+NR_033714.1"; transcript_id "NR_033714.1"; 	chrY,chrX
+NM_001185183.1"; transcript_id "NM_001185183.1"; 	chrY,chrX
+NM_005638.5"; transcript_id "NM_005638.5"; 	chrY,chrX
+NM_002186.2"; transcript_id "NM_002186.2"; 	chrY,chrX
+NM_176786.1"; transcript_id "NM_176786.1"; 	chrY,chrX
+NR_110561.1"; transcript_id "NR_110561.1"; 	chrY,chrX