--- a/biotradis_bacteria_tradis.xml	Wed Oct 23 10:40:28 2019 -0400
+++ b/biotradis_bacteria_tradis.xml	Fri Dec 06 10:11:20 2019 -0500
@@ -37,32 +37,32 @@
                     #end if
                     && tar cvzf insert_site_plot.tar.gz *insert_site_plot.gz
                     && tar cvzf mapped.tar.gz *mapped.bam*
-    ]]></command>
+    ]]>    </command>
     <inputs>
         <param name="input_files" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" multiple="true" label="Input files" />
-        <param name="tag" type="text" label="Tag" help="Tag to search for" />
+        <param name="tag" type="text" optional="true" label="Tag" help="Tag to search for" />
         <param name="ref" type="data" format="fasta" label="Reference geome" help="Fasta format" />
-        <param name="tag_dir" type="select" label="Tag direction" help="3 or 5(optional. default = 3)" >
+        <param name="tag_dir" type="select" label="Tag direction" help="3 or 5(optional. default = 3)">
             <option value="3" selected="true">3</option>
             <option value="5">5</option>
         </param>
-        <param name="mm" type="integer" value="0" label="Number of mismatches allowed when matching tag" help="(optional. default = 0)" />
-        <param name="m" type="integer" value="30" label="Mapping quality cutoff score" help="(optional. default = 30)" />
-        <param argument="--smalt_k" type="integer" value="" optional="True" label="Custom k-mer value for SMALT mapping" help="(optional)" />
-        <param argument="--smalt_s" type="integer" value="" optional="True" label="Custom step size for SMALT mapping" help="(optional)" />
-        <param argument="--smalt_y" type="float" value="0.96" label="Custom y parameter for SMALT" help="(optional. default = 0.96)" />
-        <param argument="--smalt_r" type="integer" value="-1" label="custom r parameter for SMALT" help="(optional. default = -1)" />
+        <param name="mm" type="integer" value="0" label="Number of mismatches allowed when matching tag" />
+        <param name="m" type="integer" value="30" label="Mapping quality cutoff score" />
+        <param argument="--smalt_k" type="integer" value="" optional="True" label="Custom k-mer value for SMALT mapping" />
+        <param argument="--smalt_s" type="integer" value="" optional="True" label="Custom step size for SMALT mapping" />
+        <param argument="--smalt_y" type="float" value="0.96" label="Custom y parameter for SMALT" />
+        <param argument="--smalt_r" type="integer" value="-1" label="Custom r parameter for SMALT" />
         <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="verbose debugging output" help="(Default:No)" />
     </inputs>
 
     <outputs>
         <data name="insert_size_plots" format="tar.gz" label="${tool.name} on ${on_string}: Insert size plot" from_work_dir="insert_site_plot.tar.gz"/>
-        <data name="mapped_bam" format="tar.gz" label="${tool.name} on ${on_string}: Insert size plot" from_work_dir="mapped.tar.gz"/>   
-        <data name="fastq_stats" format="txt" label="${tool.name} on ${on_string}: Fastq Stats" from_work_dir="fastqs.stats"/> 
+        <data name="mapped_bam" format="tar.gz" label="${tool.name} on ${on_string}: Insert size plot" from_work_dir="mapped.tar.gz"/>
+        <data name="fastq_stats" format="txt" label="${tool.name} on ${on_string}: Fastq Stats" from_work_dir="fastqs.stats"/>
     </outputs>
-  
+
     <help>
-    <![CDATA[
+        <![CDATA[
         Run a TraDIS analysis. This involves:
         1: filtering the data with tags matching that passed via -t option
         2: removing the tags from the sequences
@@ -88,6 +88,7 @@
         -v        : verbose debugging output
 
         Documentation can be found at `site <https://github.com/sanger-pathogens/Bio-Tradis>`_.
-    ]]></help>
+    ]]>    </help>
+    <expand macro="citations" />
 
 </tool>