--- a/samtools_phase.xml	Wed Nov 11 12:53:49 2015 -0500
+++ b/samtools_phase.xml	Tue May 09 11:18:03 2017 -0400
@@ -1,12 +1,13 @@
-<tool id="samtools_phase" name="Call and phase" version="2.0">
+<tool id="samtools_phase" name="Call and phase" version="2.0.1">
     <description>heterozygous SNPs</description>
     <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"></expand>
-  <expand macro="stdio"></expand>
-  <expand macro="version_command"></expand>
-    <command>samtools phase -b "phase_wrapper"
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+    samtools phase -b phase_wrapper
         #if str($option_set.option_sets) == 'advanced':
             ${option_set.ignore_chimeras}
             -k $option_set.block_length
@@ -15,10 +16,13 @@
             -D $option_set.read_depth
             ${option_set.drop_ambiguous}
         #else
-            -k 13 -q 37 -Q 13 -D 256
+            -k 13
+            -q 37
+            -Q 13
+            -D 256
         #end if
-        "$input_bam" &gt; "$phase_sets"
-    </command>
+        '$input_bam' > '$phase_sets'
+    ]]></command>
     <inputs>
         <param format="bam" name="input_bam" type="data" label="Select dataset to phase"/>
         <conditional name="option_set">
@@ -28,12 +32,12 @@
             </param>
             <when value="default" />
             <when value="advanced">
-                <param name="block_length" type="integer" value="13" label="Maximum length for local phasing" />
-                <param name="min_het" type="integer" value="37" label="Minimum Phred-scaled level of detail to call a heterozygote" />
-                <param name="min_bq" type="integer" value="13" label="Minimum base quality to be used in het calling" />
-                <param name="read_depth" type="integer" value="256" label="Read depth" />
-                <param name="ignore_chimeras" type="boolean" truevalue="-F" falsevalue="" checked="False" label="Do not attempt to fix chimeric reads" />
-                <param name="drop_ambiguous" type="boolean" truevalue="-A 1" falsevalue="" checked="False" label="Drop reads with ambiguous phase" />
+                <param name="block_length" argument="-k" type="integer" value="13" label="Maximum length for local phasing" />
+                <param name="min_het" argument="-q" type="integer" value="37" label="Minimum Phred-scaled level of detail to call a heterozygote" />
+                <param name="min_bq" argument="-Q" type="integer" value="13" label="Minimum base quality to be used in het calling" />
+                <param name="read_depth" argument="-D" type="integer" value="256" label="Read depth" />
+                <param name="ignore_chimeras" argument="-F" type="boolean" truevalue="-F" falsevalue="" checked="False" label="Do not attempt to fix chimeric reads" />
+                <param name="drop_ambiguous" argument="-A" type="boolean" truevalue="-A 1" falsevalue="" checked="False" label="Drop reads with ambiguous phase" />
             </when>
         </conditional>
     </inputs>
@@ -81,50 +85,10 @@
             <output name="chimera" file="empty_file.bam" compare="contains" />
         </test>
     </tests>
-    <help>
+    <help><![CDATA[
 **What it does**
 
-Call and phase heterozygous SNPs
-    
-------
-
-.. list-table:: **Options**
-   :widths: 5 5 40 10
-   :header-rows: 1
-
-   * - Flag
-     - Type
-     - Description
-     - Default
-   * - -k
-     - INT
-     - Block length
-     - 13
-   * - -b
-     - STR
-     - Prefix of BAM file output
-     - *null*
-   * - -q
-     - INT
-     - Minimum het phred-LOD
-     - 37
-   * - -Q
-     - INT
-     - Min base quality in het calling
-     - 13
-   * - -D
-     - INT
-     - Max read depth
-     - 256
-   * - -D
-     - BOOLEAN
-     - Do not attempt to fix chimeras
-     - *off*
-   * - -A
-     - BOOLEAN
-     - Drop reads with ambiguous phase
-     - *off*
-
-    </help>
-    <expand macro="citations"></expand>
+Call and phase heterozygous SNPs.
+    ]]></help>
+    <expand macro="citations"/>
 </tool>