--- a/samtools_calmd.xml	Tue Apr 21 15:13:37 2015 -0400
+++ b/samtools_calmd.xml	Tue May 09 11:18:11 2017 -0400
@@ -1,26 +1,31 @@
-<tool id="samtools_calmd" name="CalMD" version="2.0">
-  <description>recalculate MD/NM tags</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"></expand>
-  <expand macro="stdio"></expand>
-  <expand macro="version_command"></expand>
+<tool id="samtools_calmd" name="CalMD" version="2.0.1">
+    <description>recalculate MD/NM tags</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
     <command><![CDATA[
         #if str( $reference_source.reference_source_selector ) == "history":
             #set ref_fa = 'ref.fa'
-            ln -s "${reference_source.ref_fasta}" ref.fa && samtools faidx ref.fa &&
+            ln -s '${reference_source.ref_fasta}' ref.fa &&
+            samtools faidx ref.fa &&
         #else:
             #set ref_fa = str( $reference_source.ref_fasta.fields.path )
         #end if
+
         samtools calmd
-        #if str($option_set.option_sets) == 'advanced':
-            $option_set.change_identical $option_set.modify_quality $option_set.compute_cap $option_set.extended_baq
-        #end if
-        -b "$input_bam" "$ref_fa" > "$calmd_output" ]]>
-    </command>
+            #if str($option_set.option_sets) == 'advanced':
+                $option_set.change_identical $option_set.modify_quality $option_set.compute_cap $option_set.extended_baq
+            #end if
+            -b
+            '$input_bam'
+            '$ref_fa'
+            > '$calmd_output'
+    ]]></command>
     <inputs>
-        <param format="bam" name="input_bam" type="data" label="BAM file to recalculate" />
+        <param name="input_bam" type="data" format="bam" label="BAM file to recalculate" />
         <conditional name="reference_source">
             <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
                 <option value="cached">Use a built-in genome</option>
@@ -29,7 +34,7 @@
             <when value="cached">
                 <param name="ref_fasta" type="select" label="Using reference genome">
                     <options from_data_table="fasta_indexes">
-                        <filter type="data_meta" column="0" key="dbkey" ref="input_bam" />
+                        <filter type="data_meta" column="1" key="dbkey" ref="input_bam" />
                         <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
                     </options>
                 </param>
@@ -45,26 +50,26 @@
             </param>
             <when value="default" />
             <when value="advanced">
-                <param name="change_identical" type="boolean" truevalue="-e" falsevalue="" checked="False" label="Change identical bases to '='" help="-e"/>
-                <param name="modify_quality" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Modify the quality string" help="-A"/>
-                <param name="compute_cap" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Compute BQ or cap baseQ by BAQ" help="-r"/>
-                <param name="extended_baq" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Extended BAQ for better sensitivity" help="-E"/>
+                <param name="change_identical" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="False" label="Change identical bases to '='" />
+                <param name="modify_quality" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Modify the quality string" />
+                <param name="compute_cap" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Compute BQ or cap baseQ by BAQ" />
+                <param name="extended_baq" argument="-E" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Extended BAQ for better sensitivity" />
             </when>
         </conditional>
     </inputs>
     <outputs>
-        <data format="bam" name="calmd_output" label="${tool.name} on ${on_string}" />
+        <data name="calmd_output" format="bam" label="${tool.name} on ${on_string}" />
     </outputs>
     <tests>
         <test>
-            <param name="option_sets" value="default" /> 
+            <param name="option_sets" value="default" />
             <param name="input_bam" value="phiX.bam"/>
             <param name="reference_source_selector" value="history" />
             <param name="ref_fasta" value="phiX.fasta" />
             <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" />
         </test>
         <test>
-            <param name="option_sets" value="advanced" /> 
+            <param name="option_sets" value="advanced" />
             <param name="change_identical" value="true" />
             <param name="extended_baq" value="true" />
             <param name="input_bam" value="phiX.bam"/>
@@ -73,27 +78,21 @@
             <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" />
         </test>
     </tests>
-    <help>
+    <help><![CDATA[
 **What it does**
 
-Generates the MD tag using ``samtools calmd`` command. If the MD tag (see SAM format refernce below for explanation of SAM/BAM tags) is already present, this command will give a warning if the MD tag generated is different from the existing tag. Outputs a BAM file. The command has the following options::
+Generates the MD tag using the ``samtools calmd`` command. If the MD tag (see SAM format reference below for explanation of SAM/BAM tags) is already present, this command will give a warning if the MD tag generated is different from the existing tag. Outputs a BAM file.
 
-  -e       change identical bases to '='
-  -A       modify the quality string
-  -r       compute the BQ tag (without -A) or cap baseQ by BAQ (with -A)
-  -E       extended BAQ for better sensitivity but lower specificity
-  
 -----
 
 **NM and MD tags**
 
-From SAM format specification::
+From the SAM format specification::
 
   MD (string)  String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)*7
   NM (indeger) Edit distance to the reference, including ambiguous bases but excluding clipping
-  
-See refernces for more information about SAM format tags.
 
-    </help>
-    <expand macro="citations"></expand>
+See references for more information about SAM format tags.
+    ]]></help>
+    <expand macro="citations"/>
 </tool>