--- a/bwa-mem.xml	Tue Jan 19 11:20:59 2016 -0500
+++ b/bwa-mem.xml	Fri Dec 30 08:11:12 2016 -0500
@@ -26,6 +26,10 @@
 
     #if str( $analysis_type.analysis_type_selector ) == "pacbio":
       -x pacbio
+    #elif str( $analysis_type.analysis_type_selector ) == "ont2d":
+      -x ont2d
+    #elif str( $analysis_type.analysis_type_selector ) == "intractg":
+      -x intractg
     #elif str( $analysis_type.analysis_type_selector ) == "full":
       #if str( $analysis_type.algorithmic_options.algorithmic_options_selector ) == "set":    ## Algorithmic options
         -k "${analysis_type.algorithmic_options.k}"
@@ -96,9 +100,7 @@
       "${fastq_input.fastq_input1}"
     #end if
 
-    | samtools view -Sb - > temporary_bam_file.bam &&
-
-    samtools sort -f temporary_bam_file.bam ${bam_output}
+    | samtools sort -O bam -o '$bam_output'
 ]]>
   </command>
 
@@ -147,7 +149,9 @@
       <param name="analysis_type_selector" type="select" label="Select analysis mode">
         <option value="illumina">1.Simple Illumina mode</option>
         <option value="pacbio">2.PacBio mode (-x pacbio)</option>
-        <option value="full">3.Full list of options</option>
+        <option value="ont2d">3.Nanopore 2D-reads mode (-x ont2d)</option>
+        <option value="intractg">4.Intra-species contigs mode (-x intractg)</option>
+        <option value="full">5.Full list of options</option>
       </param>
       <when value="illumina">
         <!-- do nothing -->
@@ -155,6 +159,12 @@
       <when value="pacbio">
         <!-- do nothing. all magic happens within <command> tag -->
       </when>
+      <when value="ont2d">
+        <!-- do nothing. all magic happens within <command> tag -->
+      </when>
+      <when value="intractg">
+        <!-- do nothing. all magic happens within <command> tag -->
+      </when>
       <when value="full">
         <conditional name="algorithmic_options">
           <param name="algorithmic_options_selector" type="select" label="Set algorithmic options?" help="Sets -k, -w, -d, -r, -y, -c, -D, -W, -m, -S, -P, and -e options.">

--- a/bwa.xml	Tue Jan 19 11:20:59 2016 -0500
+++ b/bwa.xml	Fri Dec 30 08:11:12 2016 -0500
@@ -218,9 +218,7 @@
       "${reference_fasta_filename}" first.sai "${input_type.bam_input}"
     #end if
 
-    | samtools view -Sb - > temporary_bam_file.bam &&
-
-    samtools sort -f temporary_bam_file.bam ${bam_output}
+    | samtools sort -O bam -o '$bam_output'
 ]]>
   </command>
 

--- a/bwa_macros.xml	Tue Jan 19 11:20:59 2016 -0500
+++ b/bwa_macros.xml	Fri Dec 30 08:11:12 2016 -0500
@@ -1,7 +1,7 @@
 <macros>
   <import>read_group_macros.xml</import>
 
-  <token name="@VERSION@">0.7.12</token>
+  <token name="@VERSION@">0.7.15</token>
 
   <token name="@set_rg_string@">
       #set $rg_string = "@RG\\tID:" + str($rg_id)
@@ -35,7 +35,7 @@
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="@VERSION@">bwa</requirement>
-      <requirement type="package" version="1.2">samtools</requirement>
+      <requirement type="package" version="1.3.1">samtools</requirement>
     </requirements>
   </xml>
 
@@ -174,9 +174,9 @@
   2. https://www.biostars.org/
   3. https://github.com/lh3/bwa
   4. http://bio-bwa.sourceforge.net/
-  
+
   </token>
-    
+
   <token name="@dataset_collections@">
 ------
 

--- a/tool_dependencies.xml	Tue Jan 19 11:20:59 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="bwa" version="0.7.12">
-        <repository changeset_revision="6af9b24ddeee" name="package_bwa_0_7_12" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="samtools" version="1.2">
-        <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-     </package>
-</tool_dependency>