--- a/mitokmer.xml	Mon Apr 22 09:37:19 2019 -0400
+++ b/mitokmer.xml	Thu Apr 25 07:59:05 2019 -0400
@@ -5,41 +5,40 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
-	#if $reads.reads_select == "paired"
-	#set $name = $reads.forward.name.split('.')[0].replace(' ','_')
-	#set $forward = $reads.forward
-	#set $reverse = $reads.reverse
-	#else
-	#set $name = $reads.allreads.name.split('.')[0].replace(' ','_')
-	#set $forward = $reads.allreads
-	#set $reverse = $reads.allreads
-	#end if
+        rm $__tool_directory__/R*.fastq;
+        #if $reads.reads_select == "paired"
+        #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
+        #set $forward = $reads.forward
+        #set $reverse = $reads.reverse
+        #else
+        #set $name = $reads.allreads.name.split('.')[0].replace(' ','_')
+        #set $forward = $reads.allreads
+        #set $reverse = $reads.allreads
+        #end if
         echo $name;
         echo "-=-=-";
-	#if $forward.is_of_type('fastq.gz', 'fastqsanger.gz')
-	#set $fwd = "R1.fastq.gz"
-	#set $rev = "R2.fastq.gz"
-	#else if $forward.is_of_type('fastq', 'fastqsanger')
-	#set $fwd = "R1.fastq"
-	#set $rev = "R2.fastq"
-	#else if $forward.is_of_type('fasta.gz')
-	#set $fwd = "R1.fasta.gz"
-	#set $rev = "R2.fasta.gz"
-	#else
-	#set $fwd = "R1.fasta"
-	#set $rev = "R2.fasta"
-	#end if
-	ln -s $forward $__tool_directory__/process/$fwd;
-	ln -s $reverse $__tool_directory__/process/$rev;
-	#if $reads.reads_select == "single"
-	#set $rev = "none"
-	#end if
-	mkdir $__tool_directory__/output;
-	python $__tool_directory__/kmer_read_m3.py
-	-w $__tool_directory__/
-	-d $__tool_directory__/output
-	-i $__tool_directory__/process/$fwd $__tool_directory__/process/$rev
-
+        #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz')
+        #set $fwd = "R1.fastq.gz"
+        #set $rev = "R2.fastq.gz"
+        #else if $forward.is_of_type('fastq', 'fastqsanger')
+        #set $fwd = "R1.fastq"
+        #set $rev = "R2.fastq"
+        #else if $forward.is_of_type('fasta.gz')
+        #set $fwd = "R1.fasta.gz"
+        #set $rev = "R2.fasta.gz"
+        #else
+        #set $fwd = "R1.fasta"
+        #set $rev = "R2.fasta"
+        #end if
+        ln -s $forward $__tool_directory__/$fwd;
+        ln -s $reverse $__tool_directory__/$rev;
+        #if $reads.reads_select == "single"
+        #set $rev = "none"
+        #end if
+        python $__tool_directory__/kmer_read_m3.py
+        -w $__tool_directory__
+        -d $__tool_directory__/output
+        -i $__tool_directory__/$fwd $__tool_directory__/$rev
     ]]></command>
     <inputs>
 
@@ -49,7 +48,7 @@
                 <option value="paired">Two FASTQ datasets from your history</option>
             </param>
             <when value="single">
-        	<param label="all reads" type="data" name="allreads" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz"/>
+                <param label="all reads" type="data" name="allreads" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz"/>
             </when>
             <when value="paired">
                 <param label="Forward reads" type="data" name="forward" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
@@ -70,14 +69,14 @@
     </tests>
 
     <help><![CDATA[
-  
+
 **Usage: mitokmer.py**
 
     ]]></help>
     <citations>
        <citation type="bibtex">
-	meh
+        meh
        }</citation>
     </citations>
 
-</tool>
+</tool>
\ No newline at end of file