--- a/htseq-count.xml	Wed Sep 21 10:59:41 2016 -0400
+++ b/htseq-count.xml	Fri Jan 20 15:46:13 2017 -0500
@@ -1,8 +1,8 @@
-<tool id="htseq_count" name="htseq-count" version="0.6.1galaxy2">
+<tool id="htseq_count" name="htseq-count" version="0.6.1galaxy3" profile="16.04">
     <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description>
     <requirements>
         <requirement type="package" version="0.6.1.post1">htseq</requirement>
-        <requirement type="package" version="0.1.19">samtools</requirement>
+        <requirement type="package" version="1.3.1">samtools</requirement>
     </requirements>
 
     <stdio>
@@ -23,26 +23,26 @@
     #if $samout_conditional.samout == "Yes":
         #if str( $samout_conditional.reference_source.reference_source_selector ) == "history":
             ln -s "${samout_conditional.reference_source.ref_file}" "${reference_fasta_filename}" &&
-            samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for htseq-count" >&2 &&
+            samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for htseq-count" >&2 &&
         #else:
             #set $reference_fasta_filename = str( $samout_conditional.reference_source.ref_file.fields.path )
         #end if
     #end if
-    
+
     #if $force_sort == "True":
         #if $samfile.extension == 'bam':
-            samtools sort -n "$samfile" "name_sorted_alignment" &&
+            samtools sort -n -o 'name_sorted_alignment.bam' '$samfile' &&
         #else
-            samtools view -Su -t "${reference_fasta_filename}.fai" "$samfile" | samtools sort -n - "name_sorted_alignment" &&
+            samtools view -Su -t '${reference_fasta_filename}.fai' '$samfile' | samtools sort -n -o 'name_sorted_alignment.bam' - &&
         #end if
     #end if
-    
+
     htseq-count
         --mode=$mode
         --stranded=$stranded
         --minaqual=$minaqual
-        --type="$featuretype"
-        --idattr="$idattr"
+        --type='$featuretype'
+        --idattr='$idattr'
     #if $samout_conditional.samout == "Yes":
         --samout='$__new_file_path__/${samoutfile.id}_tmp'
     #end if
@@ -55,16 +55,16 @@
         --format=$samfile.extension
         '$samfile'
     #end if
-    
+
     "$gfffile" | awk '{if ($1 ~ "no_feature|ambiguous|too_low_aQual|not_aligned|alignment_not_unique") print $0 | "cat 1>&2"; else print $0}'
          > '$counts'
         2> '$othercounts'
-    
+
     #if $samout_conditional.samout == "Yes":
         && samtools view -Su
-            -t "${reference_fasta_filename}.fai"
-            "$__new_file_path__/${samoutfile.id}_tmp"
-        | samtools sort -o - name_sorted_alignment > "$samoutfile"
+            -t '${reference_fasta_filename}.fai'
+            '$__new_file_path__/${samoutfile.id}_tmp'
+        | samtools sort -o '$samoutfile' -
     #end if
     ]]>
     </command>
@@ -179,7 +179,6 @@
             <output name="counts" file="htseq-test-paired_counts.tsv" />
             <output name="othercounts" file="htseq-test-paired_othercounts.tsv" />
         </test>
-        
         <test>
             <param name="samfile" value="htseq-test.sam" />
             <param name="gfffile" value="htseq-test.gff" />
@@ -285,7 +284,6 @@
 Public License v3. Part of the 'HTSeq' framework.
 ]]>
     </help>
-
     <citations>
         <citation type="doi">10.1093/bioinformatics/btu638</citation>
     </citations>