--- a/seqsero2.xml	Fri Nov 09 11:30:45 2018 -0500
+++ b/seqsero2.xml	Fri Nov 09 16:02:31 2018 -0500
@@ -11,7 +11,7 @@
       <requirement type="package" version="2.27.1">bedtools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-      #if $reads.reads_select == 'history'
+      #if $reads.reads_select == 'history':
       #set name = $reads.forward.name.split('.')[0].replace(' ','_')
       #set forward = $reads.forward
       #set reverse = $reads.reverse
@@ -20,36 +20,34 @@
       #set forward = $reads.coll.forward
       #set reverse = $reads.coll.reverse
       #end if
-      echo $name ;
-      #if forward.is_of_type('fastq.gz', 'fastqsanger.gz')
-      gunzip -c $forward > forward.fastq;
+        echo $name ;
+        echo "-=-=-=-=-" ;
+      #if forward.is_of_type('fastq.gz', 'fastqsanger.gz'):
+        gunzip -c $forward > forward.fastq;
       #set forward = './forward.fastq'
       #end if
-      #if reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
-      gunzip -c $reverse > reverse.fastq;
+      #if reverse.is_of_type('fastq.gz', 'fastqsanger.gz'):
+        gunzip -c $reverse > reverse.fastq;
       #set reverse = './reverse.fastq'
       #end if
-      ln -s forward.fastq ${name}_1.fastq;
-      ln -s reverse.fastq ${name}_2.fastq;
+        ln -s forward.fastq ${name}_1.fastq;
+        ln -s reverse.fastq ${name}_2.fastq;
       mkdir ./output;
-      python $__tool_directory__/SeqSero2/SeqSero2_package.py
-      -p \${GALAXY_SLOTS:-4}
-      -t 2
-      -m $mode
-      -d ./output
-      -b $maptype 
-      -i ${name}_1.fastq ${name}_2.fastq &&
-      echo "-=-=-=-=-" &&
-      cat output/SeqSero_log.txt &&
-      echo "-=-=-=-=-" &&
-      ls -lah ./output
+        python $__tool_directory__/SeqSero2/SeqSero2_package.py
+        -p \${GALAXY_SLOTS:-4}
+        -t 2
+        -m $mode
+        -d ./output
+      #if $mode == 'a':
+        -b $maptype 
+      #end if
+        -i ${name}_1.fastq ${name}_2.fastq &&
+        echo "-=-=-=-=-" &&
+        cat output/SeqSero_log.txt &&
+        echo "-=-=-=-=-" &&
+        ls -lah ./output
     ]]></command>
     <inputs>
-      
-        <param label="Analysis mode" type="select" name="mode">
-            <option value="k">k-mer mode</option>
-            <option value="a">allele mode</option>
-        </param>
         
         <conditional name="reads">
             <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
@@ -73,10 +71,17 @@
           <option value="3">3</option>
           <option value="4">4</option> -->
         <!-- </param> -->
-        <param name="maptype" type="select" label="Algorithms for BWA mapping?">
+        
+        <param label="Analysis mode" type="select" name="mode">
+            <option value="k">k-mer mode</option>
+            <option value="a">allele mode</option>
+        </param>
+
+        <param name="maptype" type="select" label="Algorithms for BWA mapping">
           <option value="mem">mem</option>
           <option value="sam">sam</option>
         </param>
+
     
 
     </inputs>